It's not unusual for DL'ed AVIs to have something wrong in some regard. I assume that's what we're talking about. Whether it's bad frames, corrupt header, variable bitrate audio, any of those can bugger a conversion.
Here's one possibility: Try another all-in-one program like The Film Machine, or DIKO (bothfree). Other people may have their own suggestions.
If you really care about doing this, get VirtualDub, I like VirtualDub MPEG2. Open the AVI in VDub (it may complain about bad audio, click OK), go to Video and click "Error Mode", then select "Conceal errors and resume decoding at next keyframe". Then scan for bad frames. When done, make sure under "Audio", that "Source Audio" is checked. Then make sure under "Video" that "Direct Stream Copy" is checked. Then under "File" save the AVI. You'll have a new AVI with CBR audio (VDub and many encoders hate VBR AVIs), a good header and masked frames. Still no guarantee it'll work, but I've made many bad files usable that way.