The title pretty much explains it...my player does the lengthy "Checking Disc Integrity" scan every time I sync now. Any particular reason why? Is it bad, something I should look into finding the source of?

Sweet...well, it's a brand new drive; so I'm 98% sure it's not that. I'll have to go through everything else though. It still functions as normal, it just goes through the disc check every sync. It's an odd check, though; because it takes about 5 minutes, and I've got a 120GB drive. Ideally, for the full check, it should take somewhere in the neighborhood of an hour. I don't have intermittent HDD problems though, so I doubt it's an IDE cable, and the solder joints on the header look sufficient. Maybe I'll figure it out.

Read the whole FAQ, specifically the last link.