The wheel should have been centered, i.e. the rim in line'd up with the center of the hub when it was built, if it is dished sightly to one side, and the brakes are setup to compensate for this, then putting the wheel back in, the opposite way, will mean that the brakes need to be re-set, or will rub. This has nothing to do with tire rotation.

Suggest that it probably time to take it to a LBS if you can't id what the issue is.