I am editing some footage from NAMM where the dialog audio came directly from a mixing board. I can line up the new audio with the video in FCP and everything plays back fine.
When I export the Quicktime movie the new audio slightly ahead of the video. The new audio was recorded in 44.1 and I converted it in Soundtrack Pro to 48 and it didn't help. I tried creating a sequence in 44.1 using the unconverted audio file and that did not help.
The Footage is from a Canon 5D and I converted it in MPEG Streamclip to Apple ProRes 422 LT. I have a brand new WD Black Caviar 2TB Internal non System OS Drive installed which has great Disk reads and Writes in SpeedTools. Is the Pro Res format unusable on a single drive HD?
I seem to have found the problem. I am using 2 RME Fireface audio interfaces and when I select them both as an aggregate device (I created) in the audio video settings it causes audio tracks that are synched to video tracks to move in and out of sync and the video to be pause at the beginning and be jerky. If I just select one RME Fireface 800 in the audio settings everything seems fine.
I have never had this problem with Logic so it took a considerable amount of time to troubleshoot. I only found the problem after editing the same footage on my laptop with no problems.
Thanks Paul for your suggestion. Maybe this will help someone else in the future.