On the joint where the soft meets the windshield, I think, there is this constant clicking, sounding a lot like the when one raises the window after it's raised to the top. The clicking comes when I drive over rough surfaces, it's so annoying!!!

Does anyone know where this is coming from exactly, and how to fix it?

 

For me, it's left clicking ... Only happens when I put up the passenger window and click the control a few times and the click assures that the window is up all the way. Happens to most late model Honda cars as well, though your case seems weird.

 

I think it's either the rubber to rubber or glass to rubber joints around the top to the window or window frame moving around while the car flexes going over bumps. I have it and it pretty much goes away if the window is down.