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Seriously, I'm a big advocate of not making irreversible changes except as a last resort but, in this instance, is there any reason not to just file a bit off each end of the axle?
"The ends of the axle must not protrude past the outside faces of the dropouts, or else the quick release will only tighten against them and leave the wheel loose -- sometimes a problem with thin stamped-steel dropouts on older bicycles. In this case, shorten the axle, or use the wheel on a bicycle with thicker dropouts."
Could it be due to the frame out of alignment or bent dropouts? Sometimes when I install the wheel it's seems off on the top by looking at the mouting hole for brake calipers. Also do I need to pull the wheel all the way back in the dropouts?