I have Keyboard Maestro 7.3.1 running on our office server (Mac mini). Ever since I updated the server to Mac OS X 10.12.1 (Sierra), along with updating my own home Mac to Sierra as well, I cannot launch the server’s Keyboard Maestro macros using their hotkey triggers when I contact the server from my home using Apple Remote Desktop (currently, version 3.8). I’ve always been able to do that before, under earlier OS X versions (El Capitan, Yosemite, etc.)
I’m afraid that behaviour is up to Apple and the VNC software. Exactly how or if it works is beyond my control.
You may have to adjust to using a different kind of trigger.