Are you absolutely, positively, 100% certain the FLAC/WAV files are valid, non-corrupt? I know it's weird that it happens at different places/times in the file, but...I've seen stranger things happen.
Also, which installer are you using? Have you tried the installer on Mike Wren's site?
What OS?
When you deleted and re-installed, did you manually delete the FLAC s/w files (most un-install utils don't un-install very well)?