Was told by a BMW NA technical rep that water should not effect the air intakes even at highway speeds. I've been up to 70-80mph in the rain on mine with no stalling whatsoever. Must be another place letting water in.
That said, with these bikes being fuel injected, it's possible that there's an error within the system on some. When you open the throttle on a fuel injected bike, it lets more air in. This air passes over a mass oxygen sensor. The sensor reads the amount of oxygen flow, tells the ECU, which in turn adjusts the fuel pump intensity/fuel nozzle spray amount to match (based on engine load and some other things). Interesting, but complex enough that if there's a problem with one part it will effect the whole system.