I take it you mean "reset" via fuse or disconnecting battery only? I tried a Master Reset on the unit, and there was no change with iPod via USB, although the iPhone4 seems to be playing nice again via Bluetooth.
Being a techie, I am determined to get this figured out before an official patch is released.
My next hypothesis is whether or not syncing AAC tracks make a difference. The first time I used my iPod, it was strictly MP3's that I synced over via iTunes.
The next sync, I had pulled some tracks off iCloud, which creates a local AAC copy of the original MP3 file that was uploaded to iCloud (I moved all the mp3's to an external drive and removed them all from iTunes to save space on the MBP).
So my guess is that the AAC files freak out the FordSYNC. I'll do some troubleshooting and post my findings.
Side note - I plugged a blank 512MB USB thumbdrive, with no media, and it indexed it in seconds.