Thanks to everyone for their suggestions. I'm going to have a closer look today and see if I can spot anything obvious. Both rails are currently free of any gunk and are lubricated so I can rule that one out, but I think my problem may be the tension of the clamping, when the handle is fully 'up' and the fence is unclamped this is where it can wobble all over the shop, when full clamped down it is solid but due to the overall wobbly-ness it's hard to get it square to the blade, so I think adjusting the tension might reduce some of this behaviour.
I shall see how i get on, I might take some shots just in case there is something I'm missing.
Cheers fella's!