EDIT:Let me try to reword this. It didn't sound right.

I used to find that I had the same problem with my Schwinn MTB. Try turning only the end of the QR skewer that looks like a lever, while holding the nut in place with the other hand. Do the same to put the wheel back on.

When I had this problem, it was because the front fork on the Schwinn required that the QR skewer be loosened considerably in order to get the wheel out. I would just spin both ends of the skewer in my rush to get the wheel out. I have found that only turning the lever end helps to keep the wheel centered when it is reinstalled because this forces you to slow down, and to make sure that the wheel is fully alligned and installed and not sitting crookedlyin the dropouts. This would cause the wheel to rub on a brake pad. Pokey is right though, it really doesn't matter what end you turn.

Hope this reads better now. When it was first typed it was in a rush, and as I read over it now, it didn't really make much sense even to me.
-Moab