It sounded to me like an alignment problem too, but since it didn't behave like that new and there was no trauma (Are you sure you didn't do anything that could have shifted the fork blades?), I can't see this as the likely culprit. Since it now shows up with the new wheels, I am going to throw out that the new front wheel is dished to one side a bit and you are compensating for this by aligning the axle in the fork so the rim looks like it has proper alignment. Making sure the axle is seated in the DOs is the first thing you should do. Second, be aware that crowning of roads may cause similar behavior so you may want to look for a level parking lot to try a test.
Also see this article by Jobst Brandt:
http://sheldonbrown.com/brandt/pull-side.html