2002 Ford Thunderbird Leaking windows

I have a 2002 Tbird. It too leaks at car washes which I can understand but does not leak in the rain. It should not leak at all at the seal on top since the window goes inside the upper roof track. Is the window going all the way up into the track? The Tbirds have an electronic control window system that lowers the window when you pull the door handle so it clears the track. Sometimes they stop working properly and do not go up all the way. They tend to loose the programing. I used to take it to the dealer until I read in the manual that if you lower the window all the way down hold the down button for three seconds then raise it all the way up and hold the buttton again and lower it down again it resets the programing and the window closes fine. I have to do this at least one a month especially when I have the hard top off and we are lowering and raising the rag top.