If you figure this out, let me know. I had the same problem for weeks and weeks this fall. The problem appears to have solved itself at this point, though I have no idea why or how. Definitely not coming from AC system in my truck either. Same issue - pull the mats and everything looks great. Put the mats back in and see condensation on the bottom of the mats and the carpet feels damp.
I have a theory that it had something to do with parking my truck with the front end facing downhill, which I was doing all fall to avoid hickory nut damage on the front end of my truck (they just fall harmlessly into the bed). I just don't know what it could be from. As of now, everything appears fixed so I am just running with it but there has to be some reason for it.