I have a sequence with Apple Pro Res files, along with files that I exported via After Effects that are Apple Pro Res as well. I have a number of video filters that I'm adding on to each clip, 6 or 7. Without the video filters, all of the clips playback fine. However, when I add the video filters on to each clip, the Pro Res files that I exported from After Effects playback with a stutter. This stutter persists through exporting the quicktime. All of the files, and the sequence, are 23.98, and all of the clips are Pro Res HQ. This is done vie FCP 7.
Are the AE clips 23.98 or 23.976? In Ae you have to set the actual frame rate which is 23.976. FCP calls it 23.98 but it is actually 23.976. People have reported clip stuttering due to this before.
Another possibility is that your hard drives are not keeping up. What are your drives and how are they connected. If you want to test AJA and Blackmagic make free downloadable speed disk testing software.