To everyone who has this issue;
You need to do a Restore in iTunes on your iPad. Once you do that DO NOT reinstall from a backup. You need to select 'Set up new device.'
I guarantee this will fix your problems. I went from a 3 hour+ backup to about 4 minutes. I synced my entire iTunes Library, over 11 gigs, in less than 15 minutes.
Trust me, this works.
This is true but it is not a fix for everyone. If some are using an older version of iToner, they can restore and restore but they will still have the same problem. The fix is to either delete the iToner.bundle or upgrade to the newest version of iToner. Also, you can disable backups via the software at the link I posted.