Everything is Sorted!
The release of iTunes 11.0.2 and iOS 6.1.2 for my iPhone 4, seems to have sorted everything. I can now sync music, films and photos between my MacBook and my phone.
I was dubious about blindly doing the updates but decided they couldn't really mess up any further functionality so I went for it and it's sorted now.
Look in to, and take the gamble, it's up to you.