Hi guys,
I think there are two problems being identified here:
1) Mines should NOT be considered obsolete when you get Factories. Mines are supposed to upgrade to Deep Core Mines (which I haven't seen yet). Mines also gain bonuses from "boulder" planet tiles, and Factories do not (they gain bonus from the lightning bolt).
2) The upgrade bug. In Beta 2, if you had a Starport upgrade in a build queue when you saved the game, reloading the game would do two things: a) the Upgrade Starport build order would sit at 1 Week left forever;

if you delete the Upgrade Starport build order, you could never build a Starport on that planet ever again. I think some variation of this still exists in Beta 3 when you save a game with queued upgrade orders on existing non-upgraded improvements.