Are they LED or LCD keypads? I've had trouble with LED keypads doing this, especially during disarm while they alarm is going. I found that there was enough voltage drop to the keypad, stopping the panel receiving the signal.
I'd be looking at testing voltages, perhaps removing a couple of powered devices from the panel and see if the voltage rises at the keypad, removing one of the keypads etc.
Those intermittent faults are fun aren't they....
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