Hmmm.. ya got me stumped. My only suggestion would be to send (if possible) one of those problem wave files to the folks here at JRiver; but given that they are itching to release their product, they probably wouldn't have time to look at it right now.
What OS are you using? Under XP, in Windows Explorer, you can right click on the wave file and view its properties. Under the "Details" tab, if you select "Advanced," it will give you the bit rate, sample rate, # of channels, etc. Maybe you can spy something odd there.
Omni
Edit/Update:
I'd bet the farm that those wave files are simply in a format MC is not expecting. Interpreting wave files is an art, not a science. The RIFF specification, so to speak, allows for numereous things to be embedded, and unfortunately, in varying formats. Sometimes (MOST TIMES!!!) programmers take short cuts, both when creating wave files and when trying to read them.
Anyway, you can try to "resave" the wave files to a more "expected" format. Download CoolEdit 2000 (
http://www.syntrillium.com/cooledit). Open the problem wave file, and assuming it is able to read it (it should, but they take shortcuts, too, so maybe not), save it under another name. Now try your MC experiments with this new wave file.
If the new wave file causes MC no harm, and more importantly, produces a valid MP3 after converting it, then you will need to "resave" all your wave files. CoolEdit has batch conversion functionality, so this actually would not be too hard.