I have some preliminary results. They're all the same as or similar to pre-existing issues, so I'll just cheat and copy & paste most of the text from my old bug-report post.
First, in the Extra menu, when not playing a video "In Frame", you cannot stop the video by clicking in the letter-box/pillar-box "black bar" area - this occurs when running the VN in fullscreen as well.
Second, this one now occurs in both fullscreen and windowed:
Thirdly this one occurs only in windowed and also only occurs if the video resolution is higher than or equal to your desktop resolution - note that this occurs both during the story and on the Extra menu, but it does not occur with the 2004 OPs: