Discovered a leak, where is it coming from?

My bet would be you have a leak at the roof corner where the metal insert molding for the side/rear runs up onto the roof and meets the end cap seal where the roof meets the end side. This junction forms a right angle where water can "POOL" and over time will form a leak that will run down inside the walls to the floor and cause the damage you are seeing. Properly sealing that area is almost impossible because almost all the caulk normally used is not meant for "submerged" applications and once the leak has developed you might have wicking screws in that metal insert molding and trying to seal something with the main sealant as caulk is almost sure to fail at some point in the near future.

I solved this potential issue by entombing that entire corner in Eternabond ensuring it totally covered that junction down onto the roof/end cap/side areas. Not an elegant looking solution, but IMO 100% effective so here function trumps looks.

Larry