I've noticed the same issue with my roadster, but interestingly enough, more so on the driver's side. That must be where the motor/hydraulic pump is?

I haven't put the top down wet, but noticed the problem after leaving it down for over a week straight (yes...it's been a great summer here in Mich).

My sister's 99 Miata (no power top) is perfect. Could it be an issue with the power unit compressing the top too tight?