Just to confirm, I too have started having this issue (Rift CV1, Win10) about a month ago or so, that seems to happen spontaneously after watching some videos work fine, I play another video that has previously played normally, but decides to play upside down. Once that happens, any other video I start will also play upside down. Even if I close and restart DEOVR, it will occasionally still try playing videos flipped upside down. BUT, if I had used "flip vertically" setting, it remembers this setting so if it is corrected after a restart, now the I need to go back and unset the "flip vertically" setting. I have also started having some videos cause DEOVR to crash, taking me back to Oculus Home screen.
Both of these issues started at the same time, after an update but i am not 100% sure when. I believe it was about a month or a bit more back.