I think there is something that has disabled your back up feature and it has nothing to do with itunes, anyway. there is something called "itunes backup disabler" once you download it you'll have two options
1. enable backup
2. disable backup
Once you get it, click on enable and hope this will help you.
Besides what mentioned above, i like to share you a page about
You must login or register to view this content., which included transferring iPad contents to computer/iTunes.
Hopefully this works for all of you like it just worked for me!