Most often the problem is the new glass. A lot of bolters have found the new glass was not "sized" right. Most glass shops rely on you bringing in an old glass for the pattern, and if it was not an original it could cause a poor fit. I think theres a website where you can get a pattern? Instead of silicon spray, try to rub some bar soap in the glass runs. Also the window channels have some adjustment, check to make sure thier postioned right.
