This sounds as if you've paired an Apple Remote with an ID different than that of your Harmony One with your Mac. In that case, the Mac's IR port will only accept input from the Apple Remote you paired it with - and not react to Apple Remote IR commands from any other remote.

Your current pairing status is detailed at Remote Buddy Prefs > Hardware > Built-In IR receiver and - with less detail - at System Preferences > Security. You can unpair / remove the pairing in both places.

If that's not it, please run Remote Control Diagnostics (http://www.iospirit.com/labs/remotecontroldiagnostics/) and post the result.

Thanks in advance.

Best regards, 
Felix Schwarz