You need to do this first and double check the approx. frame alignment. See this link on frame alignment using just simple twine. http://sheldonbrown.com/frame-spacing.html

Next, check the dish as others have suggested. Reverse the wheel in the rear drop outs. Remember to use the chain adjuster screws on the dropouts to achieve the best center in the rear triangle you can, then remove wheel, flip and insert until the axle hits the chain adjuster screws.

Logically, a frame can NOT be aligned AND the rear wheel properly centered/dished with your situation. One thing or another is out of alignment. This is a ogical fact, unless you're doing something totally bizarre with your chain adjuster screws. This will root-cause what's going on and you can then proceed to complete the build on your bike.