My guess is that your noise is coming from RF interference (RFI), although there is a remote possibility that it could be a ground loop or other power supply issue.
What type of coax and connectors did you use on the transponder? I would recommend good quality RG-400 or RG-142 with crimp type BNC connectors. RG-58 might work, but it has a much greater chance of the signal leaking. I had a friend that tried to use Radio Shack right angle BNC connectors (they had a screw terminal for the center pin and a plastic case) for his transponder connections...talk about a recipe for disaster.
I know you said you checked grounds with an ohm meter, but that won't always identify the problem (there may be multiple ground paths). Check out the connection on the back of the transponder tray, make sure the coax shield is properly soldered to the connector. Also disconnect the coax at the antenna and check for a good ground connection between the outside of the BNC and airframe ground. If you have a bad ground caused by paint or a gasket at the antenna, the coax will become part of the antenna and radiate.
RFI can be a real pain the rear. I generally try to make sure the RF on the transmit side is only radiating from the antenna, and then I move on to the other side of the equation. The RF could be getting in through your radio, through the marker beacon, through the intercom (or any inputs connected to it), or even your ANR headset itself. You just need to be systematic, and eliminate one at a time
Good Luck,
Paige
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