IOS 6.1 update, backup 'empty'?

Hi,

I have recently upgraded to IOS 6.1 and had some problems. I shall detail them as they happened.

I used iTunes to update my iPhone 4 from 5.1.1 to 6.1. This didn't work and it got stuck in recovery mode.

I then went for a full restore to the new firmware which was successful.

I restored my phone from a backup that was made only hours before only for there to be no change to the phone. No settings, contacts, messages, photos, app settings appeared on the phone. (The restore completed with no error messages)

Confused, I synced a couple of times only to have all my apps appear but still with no data and no other settings.

I restored again assuming there was a problem with the install. Same thing.

I deleted the downloaded firmware and got a clean version from itunes. Restored, same thing.

I was worried I had lost all my data and the backup was useless so I purchased a 'iphone explorer software' to analyse my itunes backup. It seemed ok, everything was there.

I then check the file system on the phone and it looks like the restore has completed successfully as all the files are in the device backup folders.

I still have no access to my contacts, messages or any settings/user info. What can I do to rectify this? Have I missed something?