Qubes dom0 (KDE): No file manager installed.
Fedora-23 Template (Gnome): uses Nautilus
Debian-8 Template (Gnome): uses Nautilus
Whonix-12 GW & WS (KDE): uses Dolphin
hmm , what im pretty sure from is that i dont have any gnome in my Qubes. i chooses to install only KDE when i have installed Qubes into my pc. i do have plasma and plasma comes with KDE (unity with gnome). see:-
IIRC, Whonix-11 installed both Nautilus & Dophin, so upgrading that to 12 might have caused your issue?
i have started fresh whonix 12 in order to test things from ground zero. so i didnt upgrade whonix 11 to whonix 12.
but the good question is, might be that whonix and qubes (fedora) both of them having KDE installed inside them so they r crushing each other or giving multiple same shortcuts names ?