@philpw99#1693 Thanks for the info, but unfortunately the issue is deeper than that. I tried it, and all it did was remove the option to change the stereo options during playback. I've already tried adjusting all those.
The issue is that in DIrect Show, it's as if DeoVR can only see one half of the image. In Media Foundation, the aspect ratio is squashed. I see the same squashed aspect ratio in Windows Media Player, so it's some fundamental problem in how the program interprets the image, and you can't fix it by fiddling with the options.
However, thanks to your advice about transcoding in another thread, I found a workaround, which is simply to transcode them. Currently I'm using 8-bit colour and H.265, and trying to keep everything as close to the source settings as possible, but I could also try H.264.
I've googled around for a program that is able to simply read out information about the encoding of the video files themselves, but I can't find it. I don't know how you figure out all that information. I got this screenshot from PotPlayer of one of the problematic videos (it's just the technical info over a black frame):
But that doesn't even say anything about bit depth, so I have no idea. I'd be interested to know how you find out that information in the first place.