The antenna coax running along with the audio wires should only be a problem on transmit, and I have seen numerous installations where it was no problem at all.
Mine actually run together for about 6 feet, and are seperated for the next 4 feet, when they were together for the entire run they squeled like a stuck pig... (on transmit).
Sounds more like a ground problem. You didn't say what radio or intercom you have, but most have a wire from the connector directly to ground and don't only rely on the case frame. Also check tht the wires on the jacks themselves are valid. Do you have the same problem with both jacks (pilot and co-pilot) or just one?
Larry