If it was mine I would use a liberal amount of silicone behind the trim strip knowing that if I ever needed to remove the strip I would need a new one. Maybe even cap bead the strip to the glass.
If I were giving advice I say call the manufacturer with your concerns. At this point I would expect them to say its just cosmetic.
As others have mentioned, it could well be the running lights. These lights are designed to leak, or rather drain, but leak they do. There are several holes inside the lens for the wires and and screws to pass through the fixture, and there are drain holes also. The problem is that when they are not mounted on a vertical surface then the water leaks into the hole in the cab-over where the wires exit. Also, when driving in rain, water can be driven up into the drain holes of the fixture.
I used ProFlex RV caulking to seal all the holes in the light fixure and also around the fixture. Try this to see if it solves the problem. It really should be done on all cab-over RVs due to the slant design.
Oh, and I recommend never using Silcone on an RV. It doesn't stick all that well. More importantly, you can't retouch a Silicone caulking job since Silcone will not even stick to itself (nor will any other caulking stick to it). IMHO ProFlex RV is a much better caulking for RVs.
Just my 2 cents. Those rubber seals really don't seal anything. Their more for show. I had two of them go bad so I just eliminated it and put a heavy bead of a roofing product called "Through the Roof" all around. The stuff is expensive but it never cracks and seals really well. Regarding the overcab lights. Mine we're cracking because of the close proximity of the bulb to the plastic(heat). I switched to LED's end of problem. If you want to trace a water leak, one thing to try is add some red food coloring to a bucket of water, then apply some of it to suspect area's. It makes it much easier to trace and is not a permanent stain. Wipes right off.
Retired Anesthetist. Pilot with mechanic/inspection ratings.1996 Jayco C 22 foot with 460/Banks Powerpak/Bilsteins.Wife and daughter. Two cats which control my life. 1975 Ford F-250, 84 Coupe Deville, Thorp T18, tons of tools and tons of junk.
I had the same problem it wasn't the window turned out on roof where seam meet rubber roof. The seam where the front over hang meets the flat rubber roof, inside frame water follows where it leans. Clean reseal it.
I agree with comment that rubber gasket is more for show than water prevention - pics of water aren't clear on my monitor and if you have any doubt about whether window is still leaking then take the rig to the guy who installed the window and ask his opinion. If it's condensation then it's no big deal - same issue you get on home auto - just need to provide ventilation.