Popped the door card off for another look and realised that while the wire cable thing is tight against one runner, on the other runner below the motor there's quite a bit of slack. Not having replaced a regulator before, could it be a case of take everything out of the door, take motor off, replace motor and everything else back into door and it might just work perfectly once again?
Oh and I took the drivers door card off to take a look at the set up in there and found no foamy waterproofing stuff and a lot of electrical tape! In your experiences is it best to reline with thick plastic and Duck Tape?
Cheers