As you said, it's "difficult to describe the problem."
If it's super cold, you shouldn't mess with it--the plastic could crack. Still, that doesn't sound like the problem.
Was it in correctly when you bought it? I suppose it's possible that you were given the wrong size rear window. I understood they were all the same from 2007-10, but I could be wrong. Maybe a 2 door versus a 4 door or some such thing.
Assuming it's the right window, is it in or out now? If it's out, I'd try moving both zippers to the right, zip the top one up to the center effectively zipping the right side, then unzip the right side by moving the bottom zipper up to the center as well. Then zip both zippers down each side simultaneously (or down each side one side at a time, but only a few inches at a time) to close the window. Then lock in the retaining bar above the tailgate.
If that totally misses your problem, you may have to post pictures. It shouldn't be this hard. Mine is snug, but fits without any issue.