The flashing ultracube alert icon right of the toolbar prevents a programmable speaker icon alert from appearing. The speaker alert still appears on the map, but not to the right of the toolbar.

When the cube alert is (degenerately) force-blocked by sticking the charged cube in a boiler output, the speaker alert is allowed to appear.

(This mod is great fun btw, requires such wildly different ways of thinking about builds)

Weird, I don't know why that would happen, thanks for letting me know. I'll have a look. (You can disable the cube alert in the settings but I should add a hotkey for that anyway.)

It seems that this is just how factorio works - only one "custom" alert can be active at a time and script alerts take priority. In the next version you can toggle the cube alert on and off easily with a hotkey, maybe that'll help a bit.

In the next version, the cube alerts (if enabled) will check for the presence of programmable speaker alerts and share bandwidth of the single custom alert channel if necessary, by alerting only half of the time. I'll consider that a good enough fix for now.