When Stude31 helped me rebuild my left fork in the
parking lot at InZane, he was real careful to adjust the
nut on the threaded rod that goes up into the fork cap
so that the axle made a straight shot through both...
axle holes

... anywho... it seemed like the right
thing to do, but I could only guess at what the effect
would be if they weren't lined up... maybe the bike
would tend not to run straight...
-Mike