Thanks for the ideas.
Short story short, it was the skirt. Sloppy dovetails caused a bit of twist.
The fun part was figuring it out. I spent a good hour with winding sticks and shims trying to isolate the problem. Wouldnt you know it was dead simple? I put the top on just to see how much gap I had and suddenly there was no problem. Seems the weight of the top was enough to straighten it out, mostly.
@ed – I believe you called it.