I remember having a similar issue with an ipod touch, where windows would recognize it but not iTunes... My Issue was the drivers
didn't install correctly... I had to unplug the phone from the usb port, uninstall the drivers through device manager, reboot the pc and then plug the iphone back in with iTunes closed. The drivers installed fine and iTunes opened by itself, and the ipod started syncing. Hope it works for you if you haven't tried it.