I received an email this morning that a new version of iPad Transfer is now available. It must have been added to their web sight last night as it wasn't there yesterday. If you are having any issues with this software, UNINSTALL the older version and then install the new version. It seems to be important to uninstall the old version as I didn't and the problem I had was still there.
It seems this software is dependent on iTunes DLL. If so, this may pop up again with newer versions of iTunes.