One aspect of rear end alignment is whether the wheel sits vertically or not (One of the planes of alignment I mentioned before). A well centered wheel will show this. Assuming that the wheels the OP has tried are properly dished and the rim sits well centered between the chain stays then the drop outs/seat stays are not aligned. One drop out is higher then the other (or one seat stay is shorter then the other). Playing with axle spacers to get the rim to center between the seat stays will only transfer the "offness" to the chainstays and further make the wheel's contact point with the ground off line.

Like I said before if you don't fully understand frame alignment issues you need to listen to some one who does. Andy.