I've had this problem but the fitter didn't tell me untill i asked why the weights on the rear hadn't been changed. He also gave me a load of crap about the cost of adapters for the rear GS wheel so I won't be going back there. I took the rear to a car tyre fitter, he balanced it on the car wheel balancer, cost an extra fiver but at least I know it's OK now.
Never had any trouble with the front being balanced as it's a fairly conventional bike wheel.
Personally I am not sure it's worth balancing a rear wheel off the bike, by the time you get the effect of chain/shaft/bevel drive etc. the balance it probably miles out.
PS Had two sets of D607s, very nice tyre and I didn't notice any castellation (is that the same as cupping?). The Road Attacks are OK but not noticably better than the Road pilots in the wet, In the dry all the tyres I've had (D607, B/Ws, Road Pilot, Road attack) grip enough to get the GS pegs scrapping but D607s or Road Pilot are my preference in the wet.