Since the self-initialization of the windows did not work for you, you do need to go to the dealer. Some shops other than the dealer can do this, they need ISTA/P to do it.

There is a service bulletin on this this issue (happened to my car four times). What they will do is update the software on the FRM module. The hall sensor inside the window motor has lost count and the FRM software is buggy.

In order to update the FRM software they have to update the entire car (so all of the modules get updated and are at the same software release), it is a many hour process that can take 4+ hours to complete.

Once this has been done you should be okay.

Not sure if this really helps or not, but an advisor recommended to me to cycle (press to auto down, and press to auto up) the windows up and down every few weeks to keep the sensor count accurate.