I have a 2007 and have a problem with the convertible top that has been getting progressively worse.  When I put the top up or down the the waterfall piece scrapes the back window.  It's as if the entire mechanism has shifted somehow.  Additionally, the internal liner has shifted to one side and is now torn from the arm mechanism piercing through it.

I had the same problem with my 2007.  The dealer fixed it (for a while) free of charge.  It seems that some of the springs that actuate the electric top give out and the frame does not retract fully for when the waterfall swings up or down.  Mostly the scraping occurs when it is closing.  As I said, it was a temporary fix and the problem came back after a few months.  So, whenever closing the top, I reached behind me just before the waterfall would begin its swing downwards and would pull on the top towards the front.  I would then remove my hand (did not want it to get slapped by the waterfall) and the top would close down without hitting anything.