I am working with the theory that some kind of event is piling up in the Steam overlay when the editor does not swap a 3D window for a long period of time, and when it resumes rendering it must evaluate a large number of events, probably some kind of timer used by Steam. I added a timer that invalidates the main view panel every ten seconds, and have not been able to produce the problem since.
This will probably only work if at least one view panel is visible. If the editor is viewing the flowgraph or asset library, which do not use a 3D framebuffer, then I expect the problem would continue.
So, it might be fixed now, as long as one viewport is visible, but I am not sure yet.