For the sake of the community, if anyone else has this problem, after days of frustration I have found a 'workaround'
A note for anyone trying to use a 'split power supply' with this setup. Even though my supply was split prior to plugging into the UNO/Motor Shield, there still seems to be feedback through to the adapter, and thus causing glitches on the UNO, even if the jumpers are set to have each board use an independent power supply.
I am guessing (I'm sure someone else knows more) that because some of the pins are still shared through the board and shield for pwm, motor control etc that there is feedback somewhere, despite the supply being seperate.
To stop the interference coming through I had to carefully grind through the positive track on the board, right next to the servo sockets and completely isolate the servo power from the rest of the shield, then soldered header pins onto the +/- holes next to the servo pins and attached the supply to these pins instead. I then had the shield 'share' main power from the UNO with servos powered completely independently.
That completely solved the problem and it is running great now.