simple , dont get it wet.
just kidding its unfortunate that this happens, the ru8bber covering sometimes loosens up and water gets in.if you really want to try and prevent it, do hand car washes and or coin-ops. the drive thooughs arent controlable. when washing it try not to focus on that quater pannel as much. i assume you have since tightened up the rubber pannel that covers the ECU. ive heard of people using plastic bags or extra rubber to help prevent ECU damage.