What you experience is most likely a common, general problem of the Harmony: they often don't properly recognize Apple Remote codes (even the ones from the White Apple Remote) and instead of sending the correct

[press][stillPressed][stillPressed][stillPressed].. (=> one long press)

they just record and replay the raw IR signal:

[press][press][press][press][press][press].. (=> several short presses in quick succession)

The solution is to retrain the affected button(s) until the Harmony properly recognizes the respective code.

Best regards, 
Felix Schwarz