I don't have FSX but I do have P3D3 which is just about the same. I only test my repaints in P3D4.
Fired up p3d3 and installed Air Transat version and I can see radios. How are you accessing them? Maybe that's the problem? It's not something I have encountered.
Try accessing from the top menu. I would like to know.
The difference between the 2 you mention and previous versions is that I included 737-400 gauges inside the panel folder because a p3d4 user didn't seem to have those gauges in his main gauges folder. Maybe if you remove them (747-400.dll, 737-400.exp and 737-400.lib)from the panel folder and see if your method works? Then in future I will include a separate addition for p3d4 users.