all rebuilt, bled and back in use, got some cheapo kyoto pads to see it the disc will clean up, it's not warped and as minimal scoreing so it may be OK, but it defo needs to be checked and re-checked to ensure it is Ok, I'll probably change the disc anyway along with the pads just to be on the safe side.
as for cause I think mr marquez is on to something, if you look at the pic below you can see the little notches worn into the caliper, I think this as caused it to lock the pad, so I've ground it smooth so this it now moves freely, the pad indexes at the sides to this shouldn't effect the function.

So what as caused this? well I'm afraid to say it probably my fault, when I got the bike one of my jobs was stripping and rebuilding the brakes, I think when I've bebuilt the rear I haven't paid enough attention to lining the 2 sides of the caliper up, there's a small amount of movement due to the tolerences around the bolt holes, if the 2 sides aren't perfectly alinged then the retaining pin won't go through quite square and in this case as held the pad up against the caliper under pressure and eventually worn the little notches, and led to the pads sticking and ultimately overheating and destroying the pads ( and possibly the disc too), the good news is it all seems to be working as it should at the moment, but the rear brakes is one of the Aprilia's weak points ( just about good enough to pass the test but that's about it) it's so poor it's virtually a waste of time to use it while riding, so it's something i'll be looking at improving either on the winter service or sooner if I have further issues. Improving the Ape rear brake involves moving the M/C from it's current location, it's not ideally positionplace bolted to the underside of the engine right next to the exhaust (quite what they were thinking I've no idea) so the solution is to re-locate to the more traditional position behind heal plate the foot rest, I already have a Ducati brembo M/C so just need a suitable rearset to mount it on, I think it will involve some fabrication and I'd rather not have it off the road while we are having such good weather, a job for the winter me thinks.