Same problem here. I'm getting ready to do a Dicor roof touch-up. Gonna pull my Maxx-air vents also to check around vents. There's a Dicor video on You-Tube that says to clean the caulk ONLY with mineral spirits wiped on with a rag, being very careful not to allow mineral spirits to contact the rubber roof. I was thinking about doing that or maybe using a diluted bleach spray to clean the caulk before applying the touch-up.
2012 Eagle 320 RLDS
2012 Ford F-250 Crew Cab FX4, 6.7l PSD
3.55 E-locker, Timbrens