Not all of my iPhone 3GS iOS 6.0 apps will sync to iTunes

Hi There,
I apologise if this is a repeat, I tried searching on google and in here before posting.
In expansion to the subject, I recently had to wipe my PC and have been rebuilding my iTunes playlists, etc. I have also tried to sync my phone. This would download my movies and apps, etc to the PC. Unfortunately, one of my favourite apps is not syncing from my phone to iTunes even when I right-click -> Transfer purchases. I tried dragging and dropping, copying and pasting and no go.
It seems like a simple problem but the funny thing is, it copied most if not all of my other apps perfectly fine when I first plugged it in. Now it wants me to apply new settings to my phone and then tells me this app will be deleted, Continue? Heck NO!
I would be ever so grateful if any of you have a good idea besides jailbreaking my phone.
Thanks
Mike

Hi, I disabled the antivirus and the firewall. Same result
I even deleted the backup folder inside C:\Users\...\Apple Computer\MobileSync\Backup to eliminate any corruption in the old backup files.
Nothing changed: Session either times out or i get the same error message: itunes could not back up iphone because iphone disconnected. It always happens during step 3 out of 4 which is "transfering purchased apps from iphone to PC" and comes after step 2 which is backup.
My iphone 5 is not jailbroken, and is a factory unlocked phone.
Any other suggestion?
Pls help

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