Guitar Stringing Problem?

My 1st string E sounds fine, but my 2nd string B sounds almost muted when played open, on the 1st fret, second fret, and a little on the 3rd fret. when played on the 5th fret, it is in tune with my E. all the other frets sound fine. this guitar is a Fender Mexican Series Strat. I have changed the strings many times before, and i've never had this problem. and yes, the guitar has been set up, and im using the correct gauge of string. any ideas as to whats wrong? any ideas on how to fix?