That stain pictured at the low edge of the ceiling and adjacent to the skylight sure looks to be related to the roof leaking. Did you see any staining on the vent framing when you had the trim piece off?
Periodic maintenance of the RV roof calls for inspection and re-sealing as needed on a regular basis, every two years or so...
2007 Tour Master T40C
Acura MDX toad
"It takes a great deal of time to recover from any improvement..."