In order to troubleshoot the problem I'm having in my Final Cut Pro 7 edit, I've created a new project from scratch and started a test. I will describe the test to best explain the problem.
I import two video files with different content: "Clip A" and "Clip B" we will call them.
Although Clip A came from Adobe After Effects CS3, and Clip B came from some unknown place, their properties are (seemingly) exactly the same: Apple ProRes 4444, 1920x1080, 23.98 fps. In the FCP Browser Window, I can scroll right, through all of the item properties, and see that they are all matching (with the exception of things like media duration and data rate; they are two different clips).
I make a new sequence, drag in Clip A, select "Yes" to match the sequence settings to the clip settings, and then drag in Clip B right next to Clip A on video track one. Then I make a simple default crossfade between the two clips. At this point, the green bar appears in the sequence over the crossfade video, indicating that a preview render is needed. Without rendering, the video plays back and looks fine.
When I render the sequence, however, something strange happens to Clip A in the crossfade area (the rendered area). Almost every other frame is duplicated (in playback, frame by frame, and in any export) resulting in a stuttered motion. It looks similar to how a 29.97 clip would look if I placed it in this 23.98 sequence. This wasn't the case before the render. The issue only occurs in Clip A, not in Clip B.
The work around I've found is to export the FCP sequence with Clip A and Clip B prior to adding a crossfade (let's call it "Export AB"), import Export AB, cut Export AB in two, creating Clips A and B again, and then make the crossfade and render. No problem, but extra work and extra compressing.
So in my actual project, a 60 second timeline, I have a handful of "Clip A" clips that were rendered from AE and a handful of "Clip B" clips acquired from another editor. All of the "Clip A" clips have this problem anywhere there was rendering (crossfades, under graphic layers with alpha channels, etc.)
If all of the property settings appear to be the same, what could be the difference in "Clip A" that is causing this problem?