I work for a television station, and we use Flip-Factory to ingest our commercials and shows into the server. With CS6, just like with CS5.5, I export our long-form shows (SD, HD, progressive, interlaced) using H.264. The file then goes to our Flip-Factory folder, and it does it's thing. With CS5.5, we've never had a problem.
With CS6, after going through Flip-Factory, the audio in the shows start to drift out of sync after about 5 minutes into the show. By the end of the show (30 minutes), the audio is totally our of sync.
If I play the H.264 file back on a PC (before going through Flip Factory), the audio is in sync for the entire show.
Obviously, one would think this is a Flip-Factory issue, but exporting to H.264 with CS5.5 works perfectly. I don't want to use the Legacy H.264 presets in CS6, because it doesn't handle interlaced video properly (just like in CS5.5).