I don't think you were in VCP Mode 2... I know you hit the hotkey to change from 1 to 2 but it didn't seem to work, so you were in mode 1
But the VCP was answering ATC for me, I am pretty certain? Strange...
Yes, I think that this particular aircraft (a pretty complex payware addon) is set up in such a way that PF3 cannot change the radio frequencies. I was guessing that, although the radios themselves, on the pedestal, do not change, the frequencies were changing 'under the bonnet', as it were, because until the 'contact tower...' instruction things seems to work as they should (even though you say that the log shows the frequency never changed from Departure).
I am just about to fly the same a/c again and I will pay close attention to how PF3 interacts. In the end though, there is, I agree, probably not much to be done: this 777 doesn't want to let PF3 change its radios and I will have to do it manually (hard to remember, because I am so used to the VCP dealing with that in all my other aircraft!).
Thank you Dave.