Hi,

I found this same issue having bought the a/c in the sale. The way to resolve this for me is to select the same frequencies in both boxes. So box one say 122.800 and 132.600. Then the exact same in box 2. When flying online and been asked to change frequency, I only select Box 1 left hand side with the new frequency and copy this into the left hand of box 2 frequency. Both secondary frequencies  must stay the same as mentioned above.
This works for me most of the time say 90%. Another thing I do is to use the keyboard 9 key which brings up Box 2. Here I can see if there have been any strange changes without ATC moaning at me.

Hope this all makes sense!

Keith