if the 1d3v1 and 1d3v2 genre's don't match, would that be a problem?

Nope. The player software doesn't know anything about tags. and emplode only read id3v1 if id3v2 isn't available IIRC.
If you ask me, I would say that either your HD cable is bad, the IDE controller or your HD is dying, or there is simply just one single (group of) sector(s)/cylinder(s) defective on the disc, which happens to be occupied by your new song.
If I were you, I would try to get a complete boot log which shows that "irq timeout" error, and contact support.

cu,
sven