Silicone is an excellent sealant when asked to seal between two mating surfaces not exposed to weather and UV degradation. It is very poor to use as a sealant on exterior RV surfaces, it will degrade in time and the bond where it is applied will fail. This results in a bad seal and a film of silicone that must be removed for adding more sealant, even fresh silicone as it will not bond to the cured silicone.
I've had very good results with Geocel polymer sealants. They are applied just like typical silicone residential sealants, using a caulking gun. Geocel makes a few sealants for RV and mobile homes. One of these is Geocel Tripolymer Proflex RV. I used Geocel 2300 Construction Grade, a cousin of Proflex RV and results were excellent. Exposure to weather for 4 years continually has not caused any bond failure or lifting. I am now using these Tripolymer sealants in other applications as they have proved their durability to me.
Hopefully, a leaking flange or poorly positioned cover is the cause of your water intrusion. Beyond that, posts above helping to diagnose a fitting leak are the best help. A bad aluminum tank would be far down on my trouble shooting list. Good luck with that nasty water experience.