Sorry to hear you are having trouble.
The hotkeys work fine however, when I come back to my primary I can no longer click on anything.
Are you using a mouse hotkey to get back to the primary or are you just moving the mouse to it?
If you use keyboard hotkeys, do you see the same issue?
Are you certain that both PCs have the EXACT same version of Multiplicity (About Tab)?
Does a purge, and reinstall, on both PCs resolve the issue?
Stardock Support Manager