Time to fix the AVI index metadata.
Sadly, none of the tools from the "transcode" package whose names so conveniently start with "avi..." (
aviindex, for example) was able to help. But over here, I found the right command for mencoder (part of the MPlayer package, I think) that will take your audio and video stream, leave it untouched, and rewrite a new, but correctly indexed, file:
mencoder -idx input.avi -ovc copy -oac copy -o output.avi
Hope this helps!