Got a project with a bit of an odd workflow which has thrown up a bizarre problem. My side of the project was to film a presenter speaking to camera and subtitle it, which was then sent to a designer from a different company for comping with some animations. (New client, should have used us for both aspects of the job, but there you go...)
So. The designer needed to have the subtitles as a separate layer, ie, not burned on to the presenter clip. So I exported the presenter as 25fps pro res, and exported the subtitles as a 25fps animation, (With alpha).
The subtitle clip name is suffixed with the exact frame number where the subtitle should begin. So all the designer has to do is line the subtitle up to the corresponding frame on the presenter clip and voila, the subtitles should - and in FCP do - sync up.
However, they go completely out of sync in After Effects. If you go to the interpret footage panel, it says the frame rate is 1.042. What is this? And why is it not just 25fps? If I interpret the clip as 25fps in AE, it speeds it up 25x.
Without any useful information, I can only speculate. It would appear to me that you may be running something other than AE 10 (aka CS5), that you used a long-gop video layer for reference for your subtitles, then turned off the reference layer to render the alpha-channeled movie.
If any of that is true, and I don't know if it is, I would duplicate the comp in question, DELETE the reference layer (that's important) and render out a short section as a test. Import the test footage into AE, check the frame rate, and if it's okay, you should be good to proceed.
And I really hope you rendered using the AE Render Queue, and that you simply called it an export by mistake.
Sr. Promotion Producer
KCRG-TV (ABC) Cedar Rapids, IA