Maybe it's worth opening separate thread for this, as we've already gone off-topic? [1]

As for on-topic, what was changed in replacement alarm-ui (as compared to stock one), that could result in no alarms, when device boot reason is always pwr_button? Maybe replacement's author could fix it, to mimic stock behavior?

[1]
I, for one, would be very interested, to find reason for it. Checked device zillion times, hardware and software wise, yet still have no idea, what is causing this. One thing that I'm sure, though, is that it started to happen just after soldering down USB port.

OTOH, initially, only side-effect was device turning on, when battery inserted. Over time, it entered act_dead on power button boot, from time to time. It went worse over time, resulting in false charging act_dead on every boot, requiring countless battery removal and insertions + attempts to hit power button super-fast, to boot without charger.

Setting mentioned R&D flag "fixed" it, without any ill side effects. Only one thing to consider is, that now, when device is off and you plug charger in, N900 will turn itself ON, instead of entering charging act_dead. Also, you won't ever see "building up" light of diode, when you push power button - device turns on instantly. Benefits of being able to turn device ON without charger overweight those small changes in habits, still.

Vanilla alarms are working fine, though even when device is turned off.

I hope, that it's going to help with sandboxing, where replacement alarm-ui acts differently than stock one.