Can't say with certainty, but it was either beta 3 or beta 4, I think 4... To be honest I thought it was fixed in RC1, but can't really remember.
Either way, it was definitely a "known issue" and not just with LMCE. I discussed it with some of the guys here, at the time before we realised it was related to mkv. I was watching a series called Torchwood in 720p/mkv - every episode displayed this issue, sometimes just a little on the left, but often it would "grow" right out into the main part of the screen, then go back again.
Someone on the forums confirmed it was fixed in version x, and after I passed that version I have never seen it again. So I can confirm for sure that it is gone in RC2.