You made me so curious that I just installed Synergy and watched HotkeyNet receive keystrokes in the debugger. Then I said doh! because the explanation for the strange behavior turned out to be extremely simple. I think this new build will do what you want:

HotkeyNet build 56

Thanks for letting me know about this. This change will make HotkeyNet work better with a lot of programs, not just Synergy.