If you are having trouble getting a tight seal between two rigid parts, especially if those parts are flexing, vibrating, being stressed, et c. I would suggest bedding compound. 3M 4200 is the most commonly used product of this type in the marine industry. It adheres much better than other products to a greater variety of materials, especially metal and fiberglass, it will cure in almost any environment (even underwater)and it stays quite flexible when cured. This is the stuff we use to seal thru-hull fittings (holes in the bottom of the boat) where durable, water-tight seals under stress are a life-and-death proposition. It is only available in white or black, but is paintable. 3M 5200 has even better bonding properties still, but only use it on parts that will NEVER need to be removed, because you will never get it off.
At $12/tube it ain't cheap, but anywhere you might think of using caulk, this stuff will definitely get the job done.
Also, be sure to wipe down any surfaces to be sealed (regardless of sealant used) with denatured alcohol or a stronger solvent like acetone -if it won't melt the finish- until no more dirt or grease comes off on your rag. If you don't, the seal will most likely fail.