Joel are you using a cheap square to check 90 with? Not all squares are that accurate. One way to check is to take a sheet of something with a really straight edge like mdf or particle board and make a 90 on it, then flip the square over and see if it follows the line. The detents on some saws are also not very accurate, at least not from the factory.
Someone I consider a master woodworker once told me that a master woodworker is not someone who never makes mistakes. He is someone who is able to cover them up so that no one can tell.