After extensive troubleshooting, I have come to the conclusion that the retainer strips are preventing the window from expanding or contracting with the change in temperatures. At some point the expansion will overcome the retainer and the result is a loud popping sound.
My current retaining strips are very brittle and almost impossible to remove. I'm going to spray the new strips with silicone before installing them. Hopefully they will be more pliable and allow the expansion that's needed.
