Taran-
First thing I would do is find out if it will clean off with a hotter solvent!
1. Try oil based paint thinner, and if that doesn't work....
2. Try either Goo-Gone, or my favorite, lacquer thinner.
It will probably need #2, if it's an adhesive (really a sealer).
Clean it off, re-wax, and see if it recurs.
If it does, you might try to seal it, as you've suggested. However, flexing of the rail and hull may break the seal eventually, and you may have to choose between
A.) periodic cleaning re-sealing, and waxing, or
B.) Removing the rub rail, cleaning the sealant off, and using another sealant.
If while employing alternative B, you can change over from rivets to stainless steel machine screws, fender washers, and Nylock nuts. There are several discussions about this on earlier threads.
Good Luck!
Joe. :teeth :thup