This happened to me a few times. One way to correct that (if it is systematically doing that all of the times right now on your system) would be to delete the current iPad backup files on you computer, then sync again. After that, the (new) initial backup will take quite a while depending on how much info you have, but the following backups will be fast. It seems like the backup structure may be too complex at some point and iTunes has problem with it.
So, go to iTunes, Preferences, Devices, highlight your iPad backup(s) and click delete. Sync again.
Have in mind to never stop a backup sync because that could place your iPad in recovery mode and you would have to restore from the last backup or reinstall everything as a new device. So be patient and wait till it finishes. Don't forget that if you deleted the backup files, you have none to go back to if something goes wrong: that new fresh backup is very important and must not be interrupted.