I think I was one of the first people to peel back the cover on mine back in early 2006 and I made the mistake of not getting a good seal with the RTV. Make sure you go around both sides of each bolt hole and let it dry the appropriate amount of time before filling.
I used the Permatex Ultra Grey sealant I believe, as that closely matched the factory sealant. As it was a brand new truck and still under warranty, I prefered to not advertise the fact that the Diff cover had been removed, so wanted it to look the same as the factory sealant.