I believe methyl hydrate removes water from suspension in fuel; it doesn't remove it from the tank, if you are using methyl hydrate it will pull the suspended water molecules from the fuel and allow it to settle in the bottom of your tank as one pool of water; as you draw your fuel down and everything starts sloshing around in your tank the water is probably making its way back to your fuel pick up and into your system; the water in a full tank of fuel with methyl added will still be there and less sloshing with a full tank wont allow it to re-distribute. I would put your boat on an slight angle for a few days and allow all the water to accumulate at one end of your tank you can access, then siphon it out.
I would also try to figure out where the water is entering the tank from; as said before; failed "O' ring on filler; vent leaking back and gasket on your sending unit. worse case could be a small crack in the tank itself allowing water and moisture in. get the tank totally clean of water, put fresh fuel in and keep an eye on it; if it is still getting water in then you have a problem; if the water problem goes away; then you have another problem. you could have gotten some bad fuel from somewhere as well.
Good Luck!