It has happened to me 5 times out of 5 deployments I did in the past 30 days that when changing a value in InitialiseSettings.php, and syncing it out, that about half the servers (possibly more) the change does not apply.
But, it works fine on mwdebug1002. And a second touch+sync it always works on the rest of the fleet as well.
This suggests there might be a resurfaced old bug and/or new bug caused by recent changes to MWConfigCacheGenerator.