Welcome to the forum! Mine does this too. I wouldn't worry about it. Every once in a while it will not go down all the way. Only not going down by like a centimeter. Then once it does, it'll make that noise. My guess is there is something inside the hatch that gets caught on it. My runner was hit in the rear before I had it. So I dont expect the window to always work perfect.
Anyway, I see your in Chattanooga? Bout time more people from here join! Any pics of your rig?