Thank you for filing this bug report. We are investigating a fix for this problem for a future update to After Effects.

The conditions under which this problem occurs had eluded us for a long time. Only recently were we able to observe the combination of factors that are required to cause this problem:
- This happens on macOS only, not on Windows.
- The After Effects UI is spread over multiple monitors.
- The Render Queue panel is in a floating window outside of the main After Effects application window.
- That floating window is on a different monitor than the main application window.
- The Render Queue panel is docked in this floating window with either the Timeline or Composition panels.
- When you start the render queue, a modal dialog (a progress dialog or a warning dialog) appears over the main application window.

When all of the above conditions are met and the modal dialog closes, the Timeline or Composition panels (whichever is docked with the Render Queue panel) will come forward and hide the Render Queue panel.

This problem appears to have existed in After Effects for a very long time, but began to occur more frequently in After Effects 13.6 and later, when behavior was added to auto-save the project when the render queue starts. The auto-save process displays a modal progress dialog, which can invoke the problem, as per above.

But the auto-save process dialog is not the only dialog that can cause this problem. Other warnings such as color depth mismatch, missing footage, or existing file names could also cause this to occur.

There are a few ways you can avoid this problem:
- Dock the Render Queue panel in the main application window, not a floating window.
- Do not dock the Render Queue in the same panel group as the Timeline or Composition panels, if they are in a floating window on a secondary monitor. (Or the Layer panel, although this panel only causes the problem if a layer of the rendering composition is open.)
- In Preferences > Auto-Save, disable “Save when starting render queue”. However, this will not prevent the problem from occurring if other warning dialogs occur.
- Sometimes, but not always, the problem will not happen if you drag the modal dialog, before it closes, from the primary monitor to the secondary monitor where the Render Queue dialog is. This is feasible for warning dialogs when it is waiting for your response, but progress dialogs like the auto-save dialog may not be visible long enough for you to do this.

I hope this helps clarify the situation and prevent some pain until we can provide a fix for the problem. We’ve been hearing reports of the problem for quite some time, but as I noted above, we weren’t able to reproduce the issue until we observed the full set of conditions that are required to cause it to happen. Now that we know these conditions, we are investigating a fix for a future update.

Thank you for filing this bug report, and for including the project.

I do reproduce a problem when I open this project on my computer. After layer 964, the layer bars (the bars representing the time span of the layer) do not draw. If I delete or shy some of the layers, the missing layers will draw.

This appears to be a bug with After Effects drawing that many layers at once. I have forwarded this bug to our developers for evaluation.

In the meantime, I would recommend any or all of following to work around this problem:
- Shy the layers that you are not currently working on.
- Pre-compose groups of layers to simplify the composition, or:
- Otherwise re-organize this composition by breaking it into smaller compositions with fewer layers.

The above steps will help not only with working around this bug, but will make the composition easier to manage.

Thanks for filing this bug report, and for sending us the project file.

Our engineers are examining the problem. Regarding the project you sent, they gave this feedback:

This problem is independent of using Trim Paths.

The problem can occur with shapes or text converted to Shapes, as in the provided project. With the CINEMA 4D renderer the Shape stroke width does not match the Classic 3D renderer – there is both a stroke symmetry shift around the path, and size can vary as well.

The stroke mismatch is typically quite small. However, the provided project has Transform > Scale set to over 300%, thereby exaggerating the problem.

To work around this you could avoid using a large scale value on the shape layer. Adding scale per shape path almost eliminates the problem visually, but is impractical to do for each shape.

Another workaround could be to maybe prep the .eps file to have a text size that avoids the need to scale the layer in After Effects after converting to shape.