if you're uisng older style backlights (like our VA), the backlight panel may be a bit thick and cause the case to bulge. the best way (imo) to fix that is just loosen the screws a little, but you've tried that it seems....
the later backlight versions basically made that bulge a non-issue. but, the bulge problem causing the screen to pop up sounds just like what you're describing (which makes me just wonder about which version you are using). might be good to just check and make sure the case isn't bulging still. really.... the screens sholdn't pop up randomly unless there is a non-flat surface. either the case, or the screen itself,
of course make sure the surface area is totally clean before application. won't stick to dirt.
can't think of any obvious tricks to tell you. they shouldn't be cut too large though, the screen panels are modeled from the originals and also with a case in-hand. tight fit, yes.
i changed the adhesive on the latest batch i got, the clear ones. if you happen to have one of those and have noticed any difference in the adhesive bond, let me know.
also, don't try super glue. it'll eat the paint off the screen protector, or at least discolor it.