Without pictures it is hard to picture. It could be a number of things. I would try a clean rag with a little mineral spirits on a small area. If it is a contaminant on the surface it will come off, if it is damage it wont. It might be a simple cleaning job, or you may need to roll on a new rubber roof. I hope it's the first.
There are a lot of very knowledgeable folks on this site, but pictures would really help to identify your issue.
2013 Palomino SolAire 317 BHSK
Nights Camped YTD: 39
TV: 13 F-150 Screw EB Max Tow, ProPride Hitch
1995 Jayco Eagle 304 BH sold- March 2013
1978 Nomad 18 sold- April 2005