I dove in pretty far - to the point of running dtrace on the flexcolor software, and it seemed to get stuck in a thread that was receiving data from the scanner

I dove in pretty far - to the point of running dtrace on the flexcolor software, and it seemed to get stuck in a thread that was receiving data from the scanner. The Firewire port is dying (well, now it seems to be dead) so this is not a software issue and more a "i'm not prepared to drop 5,000 Euro on something that may not be fixable".