Figured it out. There was an errand 'turnOffAlarm()' in my code that I had forgotten about. So even though the RTC is set to trigger every second, if the alarm itself got shut off, it will continue to fire the alarm bits, but it won't trigger it's interrupt.
On a 328p based arduino board, user interrupt 0 is wired to arduino pin 2 and user interrupt 1 is wired to arduino pin 3. So is your clock alarm wired to pin 2?
Yessir, otherwise I would never see the initial blink to begin with.
You state the need to pull-up the alarm signal, so are you doing that with an external resistor, as there is no code in the setup to enable the internal pull-up for pin 2?
Pull-up on the interrupt, yes. And the resistor is there, yep.
This was all in the code Hardware was fine. Got it sorted out. Sometimes it helps to walk away, have a shot of whiskey, then look over the code again. I don't know if the walking away or the whiskey shot is what made it happen.
Now I have to try using both alarms and see if I can make Alarm 1 turn it on, and Alarm 2 turn it off.