An easier way to go might be to batch convert the files to Quicktime movies with alpha (Animation code, millions of colors+). You could do the batch process in Adobe Media Encoder. It would be much easier than outputting all of the alphas as separate tracks from multiple files.
You might want to check the Autodesk site to see if that particular .avi format is supported with alpha. One other thing to check is that the .avi file actually has its' alpha channel. I have read that sometimes the .avi files looks as if it has an alpha (uncompressed, 32-bit), but when you bring it into After Effects to see, the alpha is white.
Joe Bourke
Owner/Creative Director
Bourke Media
http://www.bourkemedia.com
