I'm seeing a similar problem.
Immediately upon connecting to the sim (P3D5), I get the transponder nag followed by the QNH instruction.
For the first couple attempts, the hotkey '0' wouldn't work (I use VCP mode 2 but like to initiate clearance/pb/taxi comms). Even funnier, if I changed frequencies, for instance FSS, it would initiate, but then if I switched back to tower, PF3 Web Display would say "unknown frequency"!
I changed the setting that prompts the VCP to initiate comms upon connection. This appeared to work. I then reset back to the original setting (I initiate comms) and that then appeared to work....however,
I don't hear ATC (MMCZ tower in this case) instructions, nor do they show up on RemoteText. I only know what the instructions were when I hear the VCP reply, and he replies twice. After this things seem to work OK, so far...
Also had a similar issue near TOD when I requested lower; didn't hear a response from Center but the VCP acknowledged a response.
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