Pressurization
I don't know anything about the characteristics of the radar in question, but a lot of high voltage avionics equipment detest being depressurized. It is very easy to create an ionized plasma at low pressure akin to the inside of a florescent tube. If that happened in a wave guide, you aren't going to get any sort of a signal through it.
Starting point questions: Are the radomes pressurized? Are the waveguides pressurized?
Had an interesting flight in a Scooter (A-4E) a quite few years back for just this reason.