iPad can't be backed to iTunes 11 in Mountain Lion Since updating to iOS 6.1.3 I am no longer able to copy files onto iPad and can't back up to my main Mac Pro with Mountain Lion and iTunes 11.0.2. I
first thought it was the iPad, but now it's connected to my old Macbook Pro with 10.6.8 and it is backing up just fine.

Also when I try to put files onto it using the Goodreader app it creates a miniFile with the name but then stops and freezes iTunes. Also no luck with using the seperate app GoodreaderUSB.

Any ideas where to start with the troubleshooting?
Try re-installing iTunes.  Sometimes the problem could stem from there. It's quick just head to the Apple website and download a copy and it will install on top of what you have.

Silly but also try another USB port just to be safe.