I recently finished a stop motion project, created using a large number of RAW stills shot on a Canon 5D MK ii. The stop motion sequence was created in after effects, exported to pro res, then brought in to FCP 7 and dropped into a sequence that contained normal pro res footage.

The problem I encountered was that when I exported for iTunes, trying both m4v and mp4, the video looked terrible. The quality completely fell apart and the video was definitely not worthy of showing a client. These are the same settings I use every other time I output a piece for iTunes, and this is the first time I've ever experienced this problem.

I know often problems can occur when you export something that uses different frame rates within one sequence, so I made certain not to do that. Both the final cut sequence and the original After Effects sequence were edited in 23.976 timebase.

Can anyone give any ideas as to what may have caused the loss of video quality, as well as suggest any output settings that work well specifically for stop motion animation?