The problem is that the app uses OpenGL for painting, and OpenGL doesn't support the IncludeInferiors clipping mode. Fixing that properly will require getting rid of X windows for child windows, but in the meantime I have added a workaround that should work in most cases.
For those following along, translated that means: fix that works all the time blocks on the window management 'rewrite' which means we use X windows only for toplevels. Last I heard this rewrite was about 2-3 months away from completion but obviously it's not a fixed thing and could easily take longer.
The reason it's being taken slowly is exactly so these sort of regressions can be shaken out. In the absence of branching it's the only way.
thanks -mike