vent window repair

[easyrider]

I just replaced the rubber on my 68 vent windows. I followed the video from Brothers and it was very helpful. The replacement went well, with a few problems getting the rubber to seat in frame, but the problem that I ran into was; that once the vent glass was installed the rubber kept it from closing. I thought it might settle as it sat closed, but it hasn't. it seems to be because of the rubber at the front and bottom of the glass not having enough room to let the glass slip by. Has anyone else had this problem? if so, what did you do to make it close easier.