Apparently the formats are different, too.
What, exactly, are the video codecs in use with these various clips?
There are several workarounds possible and there are far more experienced video format mixers here than I so you may need to wait a day or more for a competent answer. But, if I were doing this on my Final Cut system, I'd convert all of the various video formats to a common codec with a common temporal space. that often requires careful pulldown conversions.
The formats are all the same. The video was recorded using an DV camera, so each video was AVCHD format (.mts/.mt2s). The video plays fine before compiled with the rest, but it also plays fine in the pre-comp ram preview, like I said (which is still puzzling).
When exporting to WMV, there is a slider which allows you to choose between image quality and motion quality. Should I have played with that before rendering?
Please provide the exact settings you use. Your commentrs are far too generic to make any sense of them. coulkd be data rate issues, could be frame rate mismatches or any otehr of the bazillion possible combinations of settings.
The AVCHD codec uses MPEG compression. After Effects doesn't really like that. Sometimes it acts normal, other times it runs slow, and other times weird things happen. Dave LaRonde at CreativeCOW.net explains why:
If the footage you imported into AE is any kind of the following -- footage in an HDV acquisition codec, MPEG1, MPEG2, mp4, m2t, H.261 or H.264 -- you need to convert it to a different codec.
These kinds of footage use temporal, or interframe compression. They have keyframes at regular intervals, containing complete frame information. However, the frames in between do NOT have complete information. Interframe codecs toss out duplicated information.
In order to maintain peak rendering efficiency, AE needs complete information for each and every frame. But because these kinds of footage contain only partial information, AE freaks out, resulting in a wide variety of problems.
You need to encode your video as a different file format and coded before you bring it into AE.
And Adobe agrees.
Again, I greatly apologize for my lack of knowledge.
Could you point me in the direction of a method of encoding to a different format without losing quality?
Sorry, I thought I'd responded to this earlier.
Use Adobe Media Encoder and render out a Quicktime with the PNG codec.