Since HotKeyNet is indicating that the key was sent and you have the modifiers written into the key rather than having to manually press them, the issue is most likely within the game itself. I would guess it doesn't recognize inputs when the window is not active. I would check the sendmode you are using and look through the sendmode settings in Options > Send Mode Settings

http://www.hotkeynet.com/ref/send_modes.html
http://www.hotkeynet.com/p/background_sending.html