Hey dcr,
The first thing that comes to mind is whether or not your rudder and your steering level are actually straight. If you've got your rudder down and the steering lever adjusted directly straight, is the rudder straight and if so, does it wiggle one direction or is it firmly straight? You might need to adjust your rudder a bit so that when you're telling it to go straight via the steering lever it's actually aligned to do so. I've got the old style rudder on my '05 Sport and it occasionally works itself a little loose so I have to retighten the line on one side of the rudder or it'll pull to one side like you're describing. It wasn't visibly off when the rudder was down (i.e. when the steering level was pointed straight, so was the rudder) but when you try to wiggle the rudder, the line was slack to one side, which is why when in the water and moving forward it would tilt that direction. I haven't gotten my new kayak yet, so I'm not that familiar with the new rudders, but it's worth checking out on your kayak to see.
edit: I re-read your post and I think I misinterpreted it the first time, are you saying you think your kayak itself is lopsided? If that's the case, I don't know what to tell ya!

-Dan