Yesterday I spent 6 hours trying to figure out why an animation I created in After Effects looked stutter-y or jumpy when it was added to my Final Cut sequence and exported. Well, I finally figured it out and now I kind of want to scream at Final Cut.
Apparently, Final Cut Pro (I'm using FCP 7) rounds up 23.976 to 23.98 (or more confusingly know as 24). This is usually not a problem if you just add your 23.976 footage into FCP and start cutting. My issue was that I created an animation in After Effects, check my sequence settings in FCP to see that it said 23.98 and then used 23.98 as my comp settings in After Effects. Since After Effects is really exporting 23.98, FCP was adding frames and taking out frames in order to make up the .004 difference. This doesn't seem like a lot, but it wrecked the animations. They looked like they were having trouble playing back and it was just ugly.
So, if this has happened to you and you don't want to go in and re-export every project you did in After Effects, what you can do is open up Cinema Tools, (comes with FCP 7) and batch conform every clip to 23.98. Yes, 23.98. It's confusing, but Cinema Tools is really doing 23.976, but since all this Apple software, including Quicktime, wants to round up, you'll end up with the "correct" 23.98.
Ugh. Maybe it's time to open Premiere.
Here is some more info on the issue.