I've done a LOT of MKV conversions but I can't seem to understand this. Basically, every now and then there will be ONE frame that is out of place. It's quite obvious when I'm looking through it in VirtualDub because you can see the flicker. It's always a frame from 1-2 seconds ago. Should I just assume that whoever made the original file messed up somehow? It's very odd and I don't even know how that could occur.

BTW, this is only with a limited selection of MKVs that I have, not all of them. I made sure to check that out just in case it was my codec/splitter or something.