You can't TDR antenna lines for this system because of the reciever sensitivity of the RT unit. It is over -140db if memory serves correctly. You can rebuild the connectors, build new cables or swap with another aircraft to see if it fixes the problem. A majority of these kinds of problems are the cables/connectors. Not sure where your R/T is located, or how long the cables are. I built a set of cables just for troubleshooting for several of the different platforms I worked. Also, are there any in line connectors in your aircraft?
Do you guys still have NATEC civilians?