NeoScene has announced their tool now handles the 5D mk ii video properly at 29.97 frames per second…
From their post on dvinfo.net:
“Weekend Beta of NeoScene 1.1.3
We finally found out what was going wrong with clash between Nero 7 and NeoScene, so we here is the beta that addresses that. The second big change is regarding 30.0 vs 29.97fps of the Canon 5D MkII. While NeoScene's AVCHD decoder thought the source was 29.97 when it was in fact 30.0, we now have official imbrased the 29.97 conversion. Both audio and video stream a resampled to 29.97 (no quality loss,) allowing for much easier work with other camera sources (all 29.97 or 23.976 based) and for easier export to DVD and BluRay (both 29.97 not 30fps.) If we left it as 30.0, the default 29.97 timelines and disk formats can cause issues such as frame drops, frame blending artifacts, or audio sync programs. Standardizing to 29.97 makes everyone editing life easier, so it is an automatic feature on NeoScene 1.1.3.”
On that post is a link to the beta zip file if you're interested.
Note, this is one more backup for the earlier post we made about the realization that the 5D mk ii really shoots 29.97 and not 30fps