Run the checks described in "Bad Microphone?" Sometimes, multi-pin cables can oxidize and just need cleaned or reconnected a few times under the seat or inside the fairing. this is the most likely cause of communications problems if eithe of the headsets seems to be able to hear it's own voice.
If one seat can't hear it's own voice in the headset using intercom, then the "Bad Microphone?" checks should determine that it's the mic, but it's possible the bike itself could have a problem, which would show up in those tests as well.