Apparantly, that's what it was. I reinstalled 1.3, removed the offending tracks, and tried 2.00b3 again. After fixing the metadata, the sync went fine this time, presumably because the player didn't restart during the metadata process as it had before.
So, I can hear my music again! Yay!

_~= Dearing =~_
"WAY too happy about having #99."
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_~= Dearing =~_
Gettin' back into it thanks to slimrio!