Have you installed the After Effects CS5 (10.0.1) update? That update fixes a lot of problems.
After installing that update, let us know whether you still have this problem. If so, when you respond, please give information about your computer, operating system, footage types, etc.
I installed the update, and the problem is still there.
Here's some info for you:
Mac OSX 10.6.4
Intel Core 2 Duo
Processor Speed: 2.4 GHz
Number Of Processors: 1
Total Number Of Cores: 2
Memory: 2 GB
Bus Speed: 800 MHz
I capture footage from Xbox 360 (mostly halo 3) using a hauppauge HD-PVR, which captures 1920x1080 footage in .m2ts format, converted to .mp4. (converted in same program) Render out (and change lossless) to H.264 or Quicktime DV NTSC with default settings for those formats.
If you need anymore information just let me know.
The described workflow doesn't make much sense to me. Try describing for us why you are capturing at that codec, why you are converting to that codec, what your project settings are, and why you are then downscaling so severely--trowing so much away--and converting to another frame rate.
If you can explain why you made these choices, we can probably come up with several suggestions on how to streamline your flow and possibly correct your stuttering issues.
Sorry, maybe I just misinterpreted some information I gave you. I might just be doing all the exporting the wrong way. How would you recommend going about the exporting?
Why don"t you directly use the 1920*1080 m2ts file the Hauppauge is giving you ? Try to import it directly into AE and render it to see if you still face the problem.
Does your Hauppauge allows you to capture at other resolution / framerate / codec ?