RE: 9C & rubber duckie antenae
If you modify your transmitter from the factory configuration, of course Futaba is going to say you're on your own for support. If I took my new Jeep and threw a lift kit on it and giant tires then the factory probably wont warranty it either.
I've seen them used a lot with no problems but personally I dont see the point.
I'd look more at your onboard stuff for a voltage or vibration related problem than a rubber ducky antenna but its hard to tell without testing everything involved including the power output of your transmitter.