Basically, there are semi-transparent nodes that seem to be rendered over and over without being cleared, so they become more and more opaque. There seems to be quite a lot of conditions required to reproduce. See the attached code for detailed description in comments. Summary:
- pulse with nothing dirty
- transparent stage (but scene can be opaque)
- clip applied
- something is painted in between the problematic pulses

Perhaps there is another bug. The above happens with dirty regions on. When I try to switch them off, nothing moves (not even the animated rectangle). Again, try running the attached code.