I've taken my '06 S2K through two different touchless car washes and was pleased that it didn't leak even a drop. I expected some leakage, as my last ragtop, a '99 Mustang GT, would leak a little.
If I were you, I'd take your S back to the dealer and see if they can do anything about it. Alternatively, try a different car wash...maybe the one you visited had jets that were pointed at the worst possible angle for your windows/seals.
BTW, I agree in principle with rev2sky, but I'm a pretty busy guy and don't always have an extra hour to give my S the TLC she deserves. Also, with all the rain here in Seattle, you seldom get a chance to handwash - at least in the spring, fall and winter.