Water in fuel warnings, as far as I know, are triggered by a float in the fuel filter. My F115 has a filter, mounted under the cowling, that has a small disk that floats on water, but not on fuel. The float's level is detected by some kind of microswitch, that sends a signal to the alarm (or in your case, the engine electronics, I guess.)
My water separating filter (Racor) has a bowl where you can see the water, but it doesn't trigger the alarm (it's an aftermarket thing, as far as the engine is concerned.)
Why yours would trigger at a quarter tank, I have no idea. But investigating around there might yield some sort of result.