You've probably got a leak in the hull / deck seam.
Turn the boat upside down. Take a portable vaccuum cleaner and set it to blow. Put the exhaust outlet close
to the open drain plug - you want just a little positive pressure in the hull. DO NOT OVER PRESSURIZE THE HULL! BAD THINGS WILL HAPPEN!
Paint soapy water all over the exposed hull / deck seam. If there's a leak, it'll blow bubbles. Sometimes the leak is too big to blow bubbles - those you can either feel with your hand or look for water droplets being blown up in the air.
Mark the leaky areas with a pencil and throughly rinse off the soapy water. After everything's had a chance to dry, squirt your silicone seal in the gap and smear a coating along the whole hull / deck seam. The pencil marks can be just wiped off.
I have never seen water "leak though the hull." There's always a hole.