I am also having this problem on my 4th Generation iPod Touch. It only began happening after I updated iOS from 6.0.0 to 6.0.1.
When I sync, I get the message "iTunes could not backup the iPod because the iPod disconnected". The remainder of the Sync takes place fine.
I went into the Library folder and deleted the backup that was there. Now after a failed backup there is a smaller folder in its place.
I have tried a brand new USB cable, and I have tried every USB port directly on my Mac.
I have a PPC G5 Mac running Mac OS 10.5.8. iTunes 10.6.3. iPod 4th Generation iOS 6.0.1.
This problem is driving me crazy. I remember having a similar problem years ago with my iPod Touch 2nd Gen, but I can't remember how I resolved it.
I have held off updated iOS to 6.1, but tried the other day and the update would not proceed because the backup failed.
Should I just bite the bullet and restore my iPod?
Thanks