Hm, I haven't heard of this before this thread, but it's funny how others will chime in "oh I have that too! So it's not just me?", so I'm glad you made the thread.
Very interesting. I don't quite know how to answer though, OBS shouldn't be the fault because it doesn't do anything to other programs unless you use game capture, which is the only thing that actually goes digging around in other programs.
It feels like it would have to be something related to flash's hardware acceleration (which causes it to render with directx), and drivers. If possible, could you try disabling hardware acceleration (if it's on or present, at least)?