'02 ec300 stalling in water

[ec300 2t]

I have an '02 ec300 that stalls in water crossings about 1 ft. deep or deeper. I can kick and kick it but it won't even try to refire until it has sat for about 10 minutes and then it will start like nothing ever happened-no spitting, sputtering smoke or anything. I don't think it is sucking water in the engine because my brother has an '02 ec250 and never has problems in the same water crossings as I do. I have sealed the ignition cover (which had a tremendous gap) checked all the electrical connections,sealed the spark plug boot and coil boot with silicone grease all of which has done nothing to help. I can spray the bike mercilessly with a garden hose and never have it falter or miss a beat so it is hard to diagnose the problem at home! Has anyone had a similar problem? This bike has really tested my patience from day one but I like a lot of things about it and don't want to get rid of it. HELP!