This has been a ongoing problem with the 69 windows since they were new, my dad worked at a FORD dealer back then and several times the windows were broke loose from the brackets when the cars came of the truck. My dad had a 69 mustang in the 70's and I can't count how many times he messed with the glass on that car until he finally got tired of it and changed all the glass to 70 model bolt in style. He used to rough up the area of the glass around the brackets, use a two part type glue etc.. and it never seemed to hold up. That was back in the 70's and two part glues have come a long ways. I think if I was going to try something today on the brackets I would rough up the glass and mounting channel with a 40 grit paper by hand and use 3M panel bond part #8115, this is used in the auto collision industry to bond on roofs, qtrs. etc... Again I have not tried this and in fact I am going to save myself the hassle and install the 70 bolt in glass on my 69 and take the point deduction. Just my thoughts on it.
P.S I don't know if the climate has something to do with this problem as I have noticed some southwest cars with original glass in them appear to hold up, anyone else seen this?