Bottom track jumps slightly when overlaid elements start/stop

I have a base track that’s a screen capture, and a couple tracks above containing a bunch of captions that fade in and out.

The captions are created similar to the method shown here: https://www.youtube.com/watch?v=r89SFB4Gtt0&t=293s
They are short clips of transparent color with a text filter, added to the overlaid tracks.

The issue: Whenever a caption starts, the bottom layer jumps slightly (perhaps just 1 pixel) to the side, and when the caption ends the bottom layer jumps back.

Example of the problem can be seen here: https://vimeo.com/246357529
See timestamps 0:11 or 0:16 for example. These shifts are fairly subtle but since this is a screencast (ie. mostly a totally static image) they are very noticeable.

I have multiple overlay layers since there may be multiple captions visible at once. The jump technically happens whenever the video goes from 0 to 1 or more captions, then again when it goes back to 0 captions. That is, if one caption is visible and a second one appears, there isn’t a second jump, and the jump back occurs only when both captions have ended.

I tried adding another layer consisting of just a transparent color extending the entire length of the video, with the idea that I could force it to be “jumped” for the entire length, but this didn’t work.

This appears on both the preview and the output.

Any suggestions appreciated!

Edit: Sorry, should mention that this is on OS X 10.13.1.