Just a thought Paul, but are you sure it's not an Entropy? Aeroslave made this plane and it is like a large Prophecy, looks just like it. I am not 100% certain, but if memory serves they did make them (or some) in carbon. I am not aware of anyone making a C/F Prophecy myself.
Troy is right though, I've run antennaes in full carbon fuses, with full length carbon pipes and tubes, heck carbon everything and never had any problems. And I've used both JR and Futaba, no issues period. You may want to examine your specific radio and see what the problem is, I'm guessing the tuning is drifting or the output of your Tx is fading.
Just a thought, worth what ya paid for it
-Mike