Just tried it and everything seems to be ok, upgrades are working just fine. And there are no changes related to upgrades system in the last update, so maybe you have mixed something up? If not - give me more details on how to reproduce the glitch.
I'm not seeing the option to repair planets from asteroid belts. This seems to make the "wasteland" mission kinda impossible, since sure, losing a planet means you don't have to seed it with life, but you still need to improve it above the required parameters.
Capturing enemy bug: after quitting and loading the game again all experience is lost, you have to start capturing weak enemies to be able to capture the bigger ones.
4 orders are an improvement, thought it still feels a bit constraining. Why not let the player choose? Have an option for 3,4,8 or whatever amount of orders the player wants.
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Just tried it and everything seems to be ok, upgrades are working just fine. And there are no changes related to upgrades system in the last update, so maybe you have mixed something up? If not - give me more details on how to reproduce the glitch.