Couple questions first:
Have you maintained the caulking? Seal maintenance is paramount. I inspect all my seals and caulk every 6 months. This spring when I pulled the unit out of the shop, I was looking it over and I found a gap (not on the roof) but around the outside shower compartment which I resealed and my unit is a year old.
Truck campers especially suffer from water intrusion in the frontal area (one reason why most builders have gotten away from gasketed windows facing forward, driving in the rain is like being in a tropical storm, the water is pummeling the nose of the camper.
You could have water intrusion around the AC unit, anything is possible and if it has rot, you won't see it until it starts permeating the ceiling.
What I'do, especially if you have been lax in checking the seals and caulk is do a blower door test on the unit.
Camping World offers it (for a fee), it's called a Seal Tite Test (Sael Tite Systems provide the equipment), but you can do it yourself and it's easy to do...
You need to pressurize the unit and take a bottle of soapy water and go over all the places where there is caulk or seals. The soapy water will bubble, showing an intrusion point. You mark those with a grease pencil and go back and take care of the compromised seals.
Here's how you do it...
Take a leaf blower or shop vac on 'blow' and open your pass through window (or any convient window). take a piece of cardboard and put a hole in it for the shop vac hose or leaf blower nozzle and tape that to the cardboard. Tape the cardboard to the window, sealing the opening. Start the blower, make sure all your vents are closed all of them and exit the camper and close the door. The camper will pressurize a bit. Don't take much just a little to get that air coming out through areas of compromised seals. I do mine every year like that and 6 months just going over it visually.
Hope that helps.
That will give you a real quick idea of how bad it's leaking and where because rot is a royal PITA to repair and the mold that grows in the wet spaces can be a haalth hazard too.