Sorry to say this, but silicone caulk is bad news for this purpose. It's not really a good sealant, it's really hard to remove and it leaves residue on the material that makes it hard for other stuff to attach to it.
I would get a tube of "silicone be gone" leave it on for twice as long as they recommend. scrub with scotchbrite pad and repeat. Also, a very sharp utility knife or chisel will come in handy.
Then get a roll of EternaBond. Ebay is probably the cheapest place to get it. Clean the area super well, then generously put down the EternaBond tape give it pressure and you'll be all set.
Good instructions on fixing RV roofs with EternaBond at
Small Campers Blog Post I've fixed two seam leaks with it and they're both going 5+ years strong.
Good luck and let us know how it turns out :)
