How do you know that the dropouts are actually centered on the BB shell? If the stays are both off to the left or right, that will have the effect of making them not level when you center the wheel visually.

Check the dropout centering first with at lease a string that goes from right dropout, wraps around the headtube and goes to the left dropout. If the stays are centered, the space between string and seat tube will be the same on both sides.