Well, my 05 has only 16,000 miles on it. But since I bought it in July of this year, I THINK only twice has the car left the garage where I DIDN'T lower and raise the top during the ride at least once.
No marks on my top, 'cept for the wrinkles at the sides - but they come out if I leave the top up during the week - which I do. Takes about 3 days for them to go away.
Seems like you could stand outside the car and lower the top in stages and find where something is rubbing. Anyone tried that - watch it from the outside of the car (use a, oh, broom stick or cane or walking stick to push the button and watch it fold up from the outside.
Gotta be a way to figure out what's going on!!!!