> UPDATE:
> 
> Last known working commit: 5d8c2b742c7bc105536af56b08edb5d3349412a8
> 
> Problematic commit: 189003c83ee04e1819245c861c1ba31597db537d

Upto commit 5d8c2b742c7bc105536af56b08edb5d3349412a8, system reconfigure and
reboot happens successfully.

At commit 189003c83ee04e1819245c861c1ba31597db537d, system reconfigure gives
that warning and reboot fails.