I'm having a bizarre problem with a Giant disc brake, and I've had no luck searching for a solution on here or Park Tools. My problem is that when I mount the rear wheel to be centred in the frame, the rotor rubs heavily on one side of the caliper. Then I tried mounting it so the rotor was centred in the caliper. The rubbing stopped at the brake, but then the tire was rubbing against the frame! Here's what I've tried so far:

-I tightened all the rotor mounting bolts
-I checked the trueness of the rotor, which doesn't look worse than 0.3mm out
-I pryed the pads and pistons apart (there was enough room for the rotor without rubbing)
-I checked the trueness of the wheel, which wasn't great, but can't have had more than a 2mm per side wobble
-I don't have a dish stick, but I checked the tension of the spokes with my hands, and they felt right, the DS ones being a bit tighter than the NDS ones

The only thing I can think of now is that the brakes need to be bled. Any other suggestions? Thanks

As long as you're sure that the wheel is fully seated in the dropouts, and the wheel and rotor are true and securely mounted, the caliper is the next suspect. It sounds as though you're using a different wheel from before, in which case a pad's or caliper's position may need to be adjusted slightly. If it's not just a matter of adjusting one or both pads, I'd just loosen the caliper mounting bolts a bit, center the caliper on the rotor, and retighten the mounting bolts.