1st, I would like to know that you are working with Multiplicity 4 (MP4) and not MP3.
I'm having the same issue - I had no trouble setting up CTL+ALT+Q for the primary computer, and CTL+ALT+W for the secondary. In testing, it worked like magic, CTL+ALT+W instantly changed my screen! But trying CTL+ALT+Q to return to the primary did absolutely nothing, and the only way I could escape the secondary was to shut it down.
I want to be clear on something.
Hotkeys are for Seamless connections only. What is confusing me in what you said:
'CTL+ALT+W instantly changed my screen!'
If you were talking about Seamless, I would have expected, 'Using CTRL + Alt + W moved my cursor from the Primary PC to the Secondary PC'. Is that what you mean there..?
What I suspect you mean is that you were able to get to the KVM remote with it like this with that key combo:

What will not work (again, because its a KVM connection) is a hot key combo to go back to the Primary. The reason being is that any key combo is received by the Secondary while KVM'd to it - there is no understanding of a Primary while in a KVM connection (at least not like it is with a Seamless connection).
Could it be made to work? Could a key combo be set up so that it understand that assignment to 'Primary Computer' could switch to the Primary under KVM conditions (like it does for Seamless connections)? That I will have to discuss with the developers. That said, it would take an update for that to happen - meaning, its not 'broke' now, it just doesn't function like you think it does (again, if you are expecting it to work for KVM connections).
Sean Drohan
Stardock Product Lifecycle Manager