Known Bugs

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Known Bugs
As of version 1.1, Workflower offers the ability to log activity in order to help us debug. To enable logging, go to Settings > Miscellaneous > Enable Logging (it is disabled by default). If you cannot access the settings dialog, create a file named "wf_enable_log.txt" (without quotation marks) in your Documents user folder to enable logging.
Your logfiles are to be found under:
~/Documents/Adobe/Workflower/Logging
If you want to resolve an issue, you might want to include your latest logfile when contacting customer support.
System Bugs
Sometimes, upon executing a function, the script just loads forever without executing anything.
Workaround: Hit Escape to stop the execution. If the problem persists when trying to execute the function again, please restart After Effects. Sometimes, this solves the issue. If it doesn't, please contact customer support.
Dialog Bugs
Sometimes a borderless dialog (Main Menu, Rename Layer/s, Relabel Layer/s) will not come up at all.
Workaround 1: In some instances, this is due to the fact that Workflower is unable to determine the mouse position. When you hit Escape, the panel should come up. However, if you continue to experience the issue, please restart After Effects. In some cases, this will solve the issue.
Workaround 2: If workaround 1 didn't work and you are a Windows user, you can go to Settings > Miscellaneous and set Mouse Position Calculation to External File (Advanced). This will use a different method for calculating the mouse position. For this method to work properly, please deactivate Warn User when Execting Files in AE's Scripting & Expressions Preferences.
Workaround 3: If workarounds 1 and 2 don't work for you, please contact customer support, so we can investigate the cause. For the time being, please go to Settings > Miscellaneous and set Position of Borderless Dialogs either to At Last Position or Always Centered.
(Only on Windows:) When hitting Escape on a borderless dialog (Main Menu, Relabel Layer/s, Rename Layer/s), in some instances an error message will pop up. This, however, does not affect anything.
When your mouse cursor is right at the edge of the screen (or very close to it), borderless dialogs (Main Menu, Relabel Layer/s, Rename Layer/s) might not come up.
Workaround 1: Move the mouse cursor a little bit away from the edge.
Workaround 2: If you are a Windows user, you can go to Settings > Miscellaneous and set Mouse Position Calculation to External File (Advanced). This will use a different method for calculating the mouse position which is still able to read the mouse position if it is close to the edge of the screen.
(Only on Mac + After Effects 2021 and below:) When you move the mouse cursor away from the main menu and then back to it, mouseover icons won't work anymore.
Workaround 1: Update to After Effects 2022 or higher which will fix this issue.
Workaround 2: Click on a random button, hold it, then move away from the button and let go. After that, mouseover icons will work again.
(Fixed in version 1.0.6) (Only on Mac:) On the Main Menu, no new icons will be revealed when pressing Shift, Cmd, or Option to execute additional functions. The execution of these functions works without problems, though.
Workaround: Check the help-tip to know which modifier key will execute what.
(Fixed in version 1.1) There are issues with certain monitors, most of the time when their resolution is scaled up. Borderless dialogs (Main Menu, Relabel Layer/s, Rename Layer/s) might come up at the wrong position or not come up at all.
Workaround: Open up the Settings, go to the Miscellaneous tab and change the Position of Borderless Dialogs from At Mouse Position to either At Last Position or Always Centered.
Shortcut Bugs (Single Script Mode)
(Only on Windows:) Sometimes hitting a shortcut might not work at all. An error message from Workflower will come up, telling you that you need to restart After Effects or your computer. Most of the time, restarting the computer will be necessary. Quite likely, this bug cannot be fixed since it seems to be a bug within the Adobe scripting environment. In these cases, the variable that gives information on the pressed key will not return anything. Unless Adobe isn't fixing this issue, you will need to stick to restarting After Effects or your computer.
Workaround: If you encounter too many problems when using shortcuts on Windows, switch to Individual Scripts Mode (go to Settings / Shortcuts / Shortcut Mode). You will only have a maximum of 20 shortcuts t
o assign but you will not encounter any bugs anymore.
(Only on Windows:) In very rare instances, a certain function is being executed when actually having hit the shortcut for another function.
(Only on Windows for Japanese users:) Single Script Shortcut Mode doesn't work when the OS language is Japanese. (This is due to an AE bug. It has been reported to Adobe but as long as they haven't fixed this, Japanese users will have to rely on the following workarounds.)
Workaround 1: Use Individual Scripts Shortcut Mode. It doesn't have some advantages that Single Script Mode has (like being able to set an unlimited amount of shortcuts) but it will work without a problem when the OS language is Japanese.
Workaround 2: If you really want to use Single Script Mode, you will have to switch your OS language to US or similar. Read up here for more information.

Create Matte Bugs
If you want to undo your action after drawing a parametric shape on the group header and then executing Refresh Connections to create a Group Matte from it, you create an undo state from within the execution of the function rather than before. (Note: This does not happen when drawing a bezier/custom shape path.)
Workaround: Hit Undo three times to go back to before the execution of the function.
Merge Mattes Bugs
Due to a bug of the Calculations effect used on Matte Merge layers, when setting the Blending Mode to Stencil Alpha or Silhouette Alpha, under certain circumstances a very slight transparency might become visible although the matte source layer is at 100% opacity. (Since this is an AE bug, this problem will remain until AE is fixing it.)
Workaround: Add a Curves or Levels effect to the Matte Merge layer and boost the alpha channel a bit to get rid of the transparency.
(Fixed in version 1.0.4) As of now, when changing the comp size, Matte Merge layers will not be adjusted to the new size automatically and produce weird results.
Workaround: To make the Matte Merge layer work again, you need to go to its Solid Settings and hit Make Comp Size. It is recommended to disable Affect all layers that use this solid. (Only when you are sure that no Workflower layer other than the Matte Merge layers of the comp with a new size use this solid, you may enable Affect all layers that use this solid.)
Clone & Precomp Bugs
Cloning Mode Bugs
Under very rare circumstances, the Clone & Precomp mode Faster for fewer properties can cause various errors. This only happens when you have another script installed that uses a callback function (app.onError) to display errors that happen within the application.
Workaround 1: Remove the other script from your interface and restart After Effects.
Workaround 2: If you can't remove the other script, go to the Cloning Settings and switch the Clone and Precomp Mode to Faster for more Properties. This will not cause the errors to be generated. Please note that you won't be able to use Quick Refresh Connections in that case, too. You can only use the regular Refresh Connections.
The Clone & Precomp mode Faster for more Properties invalidates the user's clipboard. Since the mode uses AE's native function Copy with Property Links, the clipboard will then contain the layers copied to the clone comp.
Workaround: If that's a problem for you, go to the Cloning Settings and switch to Faster for fewer Properties mode instead.
The Clone & Precomp mode Faster for more Properties will cause a specific problem with AE's Redo: If you undo the cloning action and then try to redo it after that, you will not be able to recreate the original state but rather a state midway through the function's execution. Other Undo/Redo states aren't affected, though. The bug happens because Workflower has to rely on a workaround in scripting in order to make use of AE's native Copy with Property Links. Unless Adobe isn't fixing this issue, Faster for more Properties will cause issues with Redo.
Workaround: If that's a problem for you, go to the Cloning Settings and switch to Faster for fewer Properties mode instead.
Expression Errors
Sometimes it may happen that expression errors come up directly after creating a Precomp Clone if the clone has been created within a Group Precomp Clone or a Group Linked Adjustment Layer. The errors come up because certain linked attributes in the clone comps/adjustment layers haven't been updated yet.
Workaround: Simply hit Refresh Connections on the new Precomp Clone and/or the higher clones/adjustment layers to fix that.
Sometimes, after creating a Precomp Clone or refreshing its connections, expression errors can come up. These errors don't have any cause, though (quite likely due to some bug within After Effects). 
Workaround: Just click on the magnifying glass icon on the expression error message to search for the errors - that way, the error message will disappear by itself since AE cannot find any actual error.
Miscellaneous Bugs
In rare instances, something within the Precomp Clone is off compared to the source layers.
Workaround 1: It might help just to execute Refresh Connections on the Precomp Clone.
Workaround 2: Sometimes issues occur because of the fact that Workflower adds an expression to the Compositing Options of every effect within the Precomp Clone. AE sometimes seems to have bugs when it comes to expressions on the Compositing Options. To get around this, unlink your Precomp Clone. That way, Workflower will copy the layers to the Precomp Clone without expressions on the Compositing Options.
When using Refresh Connections on a Precomp Clone and one or more of its contained layers has audio, potential open property tabs of the Precomp Clone layer (including tabs of potential Dependent Clones) in the timeline will be collapsed.
Workaround 1: If you have any property selected on the Precomp Clone layer in the timeline, property tabs won't be collapsed. (Tabs of Dependent Clones will be still collapsed, though.)
Workaround 2: Use Quick Refresh Connections instead of Refresh Connections. In most cases, this will not collapse the tabs. (Using this technique, tabs of Dependent Clones will not collapse too.)
(This issue probably has been solved ->) In rare instances, when using Refresh Connections on a Prime Clone, the first frame of one of the clone layers might become invisible. 
Workaround 1: Use Quick Refresh Connections instead of Refresh Connections. In most cases, this should get rid of the first invisible frame.
Workaround 2: If Quick Refresh Connections doesn't work, or you want to use the regular Refresh Connections, go to the Cloning Settings and deactivate When disabling Source Layers, set Clone Layers to 0% Opacity by Expression. Then select the clone and hit Refresh Connections to enforce the new setting. Visibility states won't be linked now but the first frame should be visible.
3D Precomp Clones are only experimental and have several limitations. You might encounter some bugs too. Check out the dedicated chapter to understand its limitations.
Linked Adjustment Layer Bugs
When using Refresh Connections on a Linked Adjustment Layer, the user's clipboard will be invalidated. Since it uses AE's native function Copy with Relative Property Links, the clipboard will then contain the effects copied to the Linked Layers.
Unfortunately, there's no workaround to this problem.
When deleting a Linked Adjustment Layer with a Calculations effect applied to it (other effects might be affected too), then execting Refresh Layout (which delete the corresponding effects on the Linked Layers) and after that undoing the deletion, After Effects will crash in a lot of circumstances. (This is an After Effects bug and it has to do with an expression that Workflower applies to the Effect Opacity of the Composition Options on every Linked Layer. If the deletion of a referenced layer in this expression is undone, After Effects almost always seems to crash. So far, this behavior has only been observed when using the Calculations effect, though.)
Workaround: Use Delete Layer / Clone / Group to delete the Linked Adjustment Layer instead. This does not seem to cause problems with Undo later.
(Fixed in version 1.1) When using Refresh Connections on a Linked Adjustment Layer, a specific problem with AE's Redo occurs: If you undo the refresh action and then try to redo it after that, you will not be able to recreate the original state but rather a state midway through the function's execution. Other Undo/Redo states aren't affected, though. The bug happens because Workflower has to rely on a workaround in scripting in order to make use of AE's native Copy with Relative Property Links. Unless Adobe isn't fixing this issue, using Refresh Connections on a Linked Adjustment Layer will cause issues with Redo.
Unfortunately, there's no workaround to this problem.
Rename Layer/s Bugs
(Only on Mac:) On the renaming panel, when flipping forward or backward through the naming levels, the new name level will not be selected (as compared to the Windows version).
Workaround: Hit Cmd+A to select the name level.
Relabel Layer/s Bugs
(Solved?) On some machines, an error message might come up when trying to open the relabel panel. This is because Workflower has to rely on a workaround to read AE's label colors. If that is the case, contact customer support with specific details about the After Effects version, language, etc., so we can fix this issue.
Workaround: To relabel groups, you can also just come up to the group header, select another label color using AE's native label dropdown, and then hit Refresh Layout to relabel the entire group.
Reveal Layer Opacity Bugs
When revealing the opacity of a layer with time remapping enabled, the Time Remap property will be revealed as well.
Unfortunately, there's no workaround to this problem.
F.A.Q.
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Outline
System Bugs
Dialog Bugs
Shortcut Bugs (Single Script Mode)
Create Matte Bugs
Merge Mattes Bugs
Clone & Precomp Bugs
Linked Adjustment Layer Bugs
Rename Layer/s Bugs
Relabel Layer/s Bugs
Reveal Layer Opacity Bugs