Forks have an interesting issue with alignment. A fork can be perfectly aligned from a steering geometry perspective, and catywumpus from a cosmetic perspective. This may be the case with your fork.

I suppose the first question to ask is, are the spaces on either side of the wheel to the fork blades equal?
What kind of fork is it? Unicrown, lugged crown?
Also, if you take the fork out and put it on the table, then measure the height of the dropouts from the table.