Ok, after trying to slog through the Incredibles, which has provided the worst playback yet (especially for audio), I tried watching and listening a bit with the messages on the screen.
main warning: buffer is 46860 late, triggering upsampling - I noticed these popping up at the same time as some of the smaller skips, either in audio, video, or both.
main warning: output PTS is out of range (335605), clearing out - This message pops up, sometimes with other warnings and sometimes clumped with other "clearing out" and "dropping buffer" messages in a row, when I get the more obvious stops in both audio and video simultaneously that feel like a reset when you're watching.
I feel like we've been sorta ignoring these, but these are at the core of the problem in some way. I probably already said this but it feels like the program is trying to play at the same time it's reading. That would explain the variance between different DVDs, as the number of skips would more heavily depend on the newness/cleanliness of the medium. Nothing I have played recently could be called a defective DVD, but ordinarily the little "fixable" errors would be caught and fixed before the buffer ran out.
It occurs to me a few minutes after writing this that you probably were aware of this all along and were just framing it differently. Hopefully my declaration of the obvious isn't insulting or anything.