You can use the Plex Behaviour that ships with Remote Buddy with any 
supported remote control. Since it exposes pretty much any keyboard 
command that I know of, you should be fine to use with any remote.

Regarding your problem: 
I think what happens in your case is that your Harmony sends a full 
button code multiple times (you mention a repeat option that you've 
set), which of course the receiver and thus Remote Buddy can only 
interpret as a button being pressed multiple times. If the Harmony 
just replays the code it was taught without understanding the 
specifics of the IR code format, that's what will happen and what will 
give you the results you observe.

What remote control are you trying to replace with the Harmony?

Have you tried using the actual remote instead of the Harmony?

Best regards, 
Felix Schwarz