If you ever do your taxes online--as I have for the past several years--please be sure to doublecheck each page before you move on to the next. In particular, please be sure to assign the state withholding from your W-2's to the proper state, and not another state you have never lived in.
I can attest to this personally, because something very similar happened to us a couple of years back. We filed online, and in the course of doing so we mistaken checked the box that, for the purposes of New York State, denotes that we are a residents of New York City or Yonkers. Doing so has a pretty, shall we say, significant effect on one's overall tax bill.
We thought we corrected it before finalizing the return and sending it through, but somehow the NYS tax people got the wrong return anyway, and claimed that we owed money for living in NYC or Yonkers (where, obviously, we have never lived -- in fact, the Wife has never been to NYC and I haven't been there since a drive-through with my father in 1985 or thereabouts). It took the better part of a year to get this cleared up.
So watch what you're clicking, and make sure you print several copies of everything you send through to your state government.