I have the same problem as this user (who never posted whether there was a solution):
Applications seem to "disappear" within containers, completely randomly. Happens with Spotify and RStudio, for example. The application keeps running fine, but I can't see it or interact with it in any way. In this screenshot, Spotify is running in the left container:
Currently running the 5.4 kernel, but I've had the same issue under 5.3, 5.2, and 4.19.
Any thoughts on how I can debug this?