gdavis

For me, the eISYIR plugin works flawlessly with the Harmony (and the SofaBaton X1/X2) using the original ISY994 code set. However, I initially ran into the exact same reliability issue you described.
The root cause comes down to how some remotes work. Some use a "toggle bit" that flips every time you press a button. For example, the first press of a remote button sends Code A, and the very next press of the same button sends Code B. This is how the remote tells the receiver the difference between a held button and a fresh button press.
The ISY994 handled this automatically. The FLIRC, however, treats them as two completely separate commands.
The fix is to record both variations for every key using the FLIRC software:
Select the key you want to program in the FLIRC app.
Press the corresponding button on your Harmony remote to record the first code.
Select the same key in the FLIRC app again.
Press the same Harmony button a second time to record the alternate code.
Since FLIRC allows multiple IR codes to map to a single keyboard key, it will now recognize the button press every single time, regardless of the toggle state. I hope this works for you.