This requires large changes to sensitive parts of the core. It's most certainly not going to be fixed in 1.0.x at all, as the risk of side effects are too big. And with the constrained development resources, it's not quite clear that we can fix it anytime soon.
Besides, nobody provided any sample file, so we cannot reproduce the problem, so we cannot fix it.
OK, i am using the latest VLC Player. i am only using it for .mkv files because now all my anime seems to be in that format. i hate it because windows media player and wmp classic both get pissy about them even with codecs. if you go to bakabt.com and download ANY mkv format anime series, watch the first episode and you should get all the way through it, but the second episode will start freezing approximately every 20 seconds. What it does on the anime is the video will freeze anywhere from a half second to 2 seconds, then it will accelerate to catch up. the problem with this, the audio keeps going, but the subtitles will only flash for a fraction of a second if they show up at all. this is where it gets real annoying, if i don't do anything with the slider, it will continue to pause the video and try to catch up for the remainder of the episode. end result: you get very choppy video, flawless audio, and impossible to read subtitles if they are even shown at all.
(i directed you to bakabt.com because any anime that is licensed will NOT be listed there)
*edit* (i have tried playing at least one episode from almost every series i have that is .mkv, the result is always the same. i have tried downloading different versions of shows encoded on different machines, it is not the video file itself.)
**edit** upon closer inspection, i have found that it is easier for the video to freeze when there is less movement on screen ie-an extended dramatic pause, a focus on an unmoving object, etc