Running from terminal using `/Applications/Synergy.app/Contents/MacOS/synergys` seemed to fix it for me.
I am guessing its something to do with the way that the Synergy frontend starts the service. The different behavior could be explained by:
- Different environment variables
- Maybe the way the process is started impacts how Accessibility API permissions (`tcc` stuff) works. Maybe the permissions were inherited from the GUI, instead of the service.