Sounds like one of two things. Either your floats are too far apart and the prop tip is too close to the water, or you're getting spray from the floats' wake and the prop is hitting that.

Probably the latter; I made a couple of strakes that fit the inside edge of the floats from about an inch behind the tips to about 3/4 of the way to the step. They cut down on the spray a good bit, although they're not a complete fix, they help a lot. The GP manual has patterns for all their float sizes, and says to make them from thin styrene plastic. I made mine from two layers of1/32 balsa, with the grains crossed to improve strength. I 'glassed them separately from the floats, then epoxied them to the floats and painted the whole thing.

Also note how far apart my floats are. The distance between each float's centerline is the same as the distance between the wheels on a land-Cub.