I can confirm this as well, the Star Trek: The Original Series BluRays (which were encoded using VC-1, even the interlaced video extras) are dropping many frames, and are a stutter fest.
I also discovered another issue which happens only in BluRay playback mode, but not in Title playback mode: blinking subtitles on some BluRays (the subtitles show and hide themselves every half second or so). An example is the Drive My Car Japanese Bluray (which has English subtitles on it too, although it does not matter, the blinking happens with both Japanese and English subtitles). If it's difficult to source it, I'll try to make a sample.