So yes, these files worked fine with 1.0.0, but now after upgrading all I get is major lag between audio and video, with audio being about 5-10 seconds ahead. I'm using CoreAVC but still the same issues.
Well..I went back to 1.0 but I realized that I think my problem isn't with the version of MediaPortal but the MKV file itself. The same file I tried playing in 1.0 and it was all choppy so I downloaded a different file of the same show and it worked flawlessly so that leads me to believe that the encode is what's important and only get from reliable sources who know what they're doing.