I recommend that all with rubber roofs check the area where the a/c's drip onto the rubber not just the caulked joints. My EPDM roof failed directly where this drip was on both a/c's. Moisture was leaking through the membrane. If you are not a full timer then you might be ok, but in my case I had 5+ years of full time use and in the south so LOTS of a/c run time.
My solution was replacing the entire roof and I definitely didn't want to spend the bucks for the same thing and expect different results the second time. I used rvroof.com and recommend this approach highly. It was about the same price as a new rubber roof and zero caulking to watch and worry about now. And since the roof is now thicker I can watch TV and actually hear it when it is raining. I also used the roof replacement as a good time to replace the skylight and crank up TV antenna that I never used. This antenna had leaked through it a time of two and I was just plain tired of this.
2006 GMC 2500HD CCSB 4x4 Duramax/Allison, Titan 52 gallon fuel tank, Prodigy Controller, B&W Companion Hitch
2010 Jayco Designer 35RLTS, Cummins/Onan RV QG 5500 EVAP, Progressive Industries EMS-PT50C, TST Systems 507 TPMS, RV Flex Armor Roof