Alert volume (not system) consistently reset to zero for unknown reason
Try completing an NVRAM / PRAM reset. This is the part of the computer that often holds these values in memory and can sometimes become the source of this type of issue....


Reboot your computer.
Hold Command + Alt + P + R
Wait until you hear the startup sound/chime a second time, during this time the computer will reboot.


If the computer does not chime a second time but instead boots up you've not pressed the shortcut quickly enough, you can press it as soon as you've pressed reboot, and sometimes need to use a wired not wireless keyboard for this.

Verify of the issue is resolved.

Further details on Apple's website