Richard,
It is kind of tricky with the mast in place. I don't know if you can peek inside where the halyards exit at the bottom to see what is going on in there. Everything is sort of a sandwich and was hopefully caulked when the mast was set. There is the hole through the deck. That should have a pipe stuck in that should have been coated with caulk (either Boat Life or 4200) The wires go down the pipe, but with a loop so rain can't run directly down the wires into the pipe and inside the overhead. I formed the loops with excess wire just before my mast was dropped into place and filled the pipe and wires with silicone. The mast step is a flat piece of aluminium that has a raised edge (1/2") the mast goes over so it can't slide around. The step is secured with 4 screws tapped into the deck. Under the fiberglass deck is a 1/4" aluminum plate that the screws thread into. I caulked under the step and the screws with 4200.
In your case, you have to determine if there is indeed a leak. After opening up things inside the boat, use a hose to flood around the deck under the mast. That will be a clue to whether or not the pipe is leaking. After that looks good, you can try and shoot water up and get it to fall onto the top of the pipe. That is the other source of leakage. I don't think the step can leak. It is on top of the solid deck surface. The screws don't go all the way through. Below the aluminum plate is some kind of synthetic solid core (not balsa or plywood there) and then the fiberglass skin of the back side of the deck surface. Water can only come in that hole through the pipe or around it. That is unless you have other penetrations other than stock like radar or something.
If you have a leak, I guess I would try getting silicone around the pipe. You could also try shooting the expandable foam up from underneath into the wire conduit (the pipe) if that is how the water comes in. Just make sure you use a long enough nozzle to really be up inside the pipe itself, otherwise you may just redirect the water somewhere else.
Good luck.
Allan