I've used the MS capture tool to capture hundreds of avi clips off of a digital video camera and never had any problems. Clips range from 3 seconds to 3 minutes in length.
In the midst of capturing several score of clips the other night, one get messed up. As you know, dv is captured at 720x480 resolution. Well, this clip was captured at 720x527, and was completed screwed up. You could drop it onto a video track in MS, put it played as garbage. Eventually, if you tried to play it in the MS Capture facility, it crashed. I was able to delete it and recapture that portion of the video with no subsequent problems.
Isn't that curious? Wonder why the capture aspect ratio got screwed up from that 1 clip in the midst of many?