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String method shows it's slightly out of true, seat tube is 3 mm closer to the drive side. :\ So I guess the frame is wonky and I can't fix that.
I'll just set-up my brakes as good as I can and keep my eyes out for a new frame. I checked the frame for cracks in the paint and other anomalies around the welds but didn't find any so I'll just hope it won't fail on me until I can afford something better.
You could take a file to the drop out and enable the axle to take a position that ensures the wheel is lined up at the brake. However, if you wanted to take a more longterm view, you could check the frame to see whether it's true (see Sheldon Brown's piece of string method for that) and also check that the drop outs are aligned (probably need yer LBS for that unless you have the right tools). If there's something seriously misaligned with the frame, then I'd be thinking about changing it - bent/crashed aluminium will have lost a lot of strength and could fail.