wet floor

i've got a 2002 B3000 extended cab, 2 door. the passenger side carpet is wet right in the middle of the floor. pulling up the carpet i saw the oval shaped floor plug and the smaller round floor plug. i pulled the oval one, ran a bead of silicone around it and replaced. the smaller round one was pulled and i noticed the hole was slightly misshapen. i straightened it as best i could with pliers, siliconed the plug and replaced hoping this cures the water thing. anyone else ever experience this and what other causes should i be looking for? there is no water on top of the rubber floor mats and the carpet up near the fire wall remains dry so i don't think it is a heater core or vent channel issue.