I can’t answer the question for you but maybe a few tips to the problem. 2 boxes doesn’t necessarily mean true redundancy.
Are the boxes exactly the same (manufacturer/model etc).
How repeatable is the problem: Can you get this to happen on the ground and outside the range of the transmitter on the offending frequency.
Is the freq at one end of the spectrum.
Are there any other possible factor for example the freq is close to the freq set on the nav box at the same time (I am thinking of some kind of harmonic interference in the AF stage). Have you tried different headsets?