serovoy
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I don't know if it's configured that way or something else... Some of the Lords of the North missions are tied to the red tier of the Order faction, which in this game wasn't an alternative to the main faction, but was a new, quite overpowered line, only for Campaigns. Apparently, the forts somehow "know" this, but the cities don't. And it's the latter that might be worse in terms of completing the Campaigns (although I don't think there was a moment where this was crucial).
If you need to fix the forts, you need to tinker with the maps. Most likely, this is in the fort settings. But I would rather make a restriction on the availability of upgrades in cities in the Campaigns (each city has such a setting).
PS: by the way, in Agrael's missions, from the third to the last, all forts are fully functional (they upgrade and transfer units), which, in general, confirms your theory that they really dug into the settings.