I cannot be absolutely sure if it was just missing event, but I upgraded both of top towers (wood and dawn’s) about same time and supply difference was less than one supply run. One hour after first tower had been upgraded properly, the dawn’s workers were still taking supplies but not actually upgrading the door. Upgrade vendor said it’s been worked on. I’m not entirely sure if the event fired up when I ordered the upgrade, but it never showed up on consecutive visits.
I have heard of this before, but then the doors not getting upgraded was attributed to badly placed siege engine on inside of our walls.