Rear disc brake rotor rubbing against caliper frame mount?
I have a 2010 Gary Fisher that Trek recently warrantied. They provided me with the entire rear triangle of a 2013 Superfly, which by all appearances seems identical to my old triangle. There are differences though. Most notably with the new drop-outs. They are deeper than the original. By just enough that I was also having your exact problem. The fix - recommended by the mechanic at my local bike shop - was a simple, external star lock washer placed in between the axle end cap and the drop-out.