I have that system. I was told by the Honda service dude that:
1 beep = You just locked the doors
2 beeps = You just unlocked the doors
3 beeps = You tried to lock the doors, but at least one is partially open
4 beeps = Since you locked the doors, something has tripped the alarm
I have verified the first three, but I had the sensitivity set so low on the alarm, I haven't been able to get 4 beeps yet. I kept the keyless entry for that function only, not the alarm.