This has to be part of StarRover's Armor Calculation Script, its just one of the things it has in it, so as far as I know its supposed to do that.
The script seemingly just "checks" the mothership HP and sees if the Shield realistically should be operating or should malfunction, since you've got below 80% HP the Script gets triggered and as such it nullifies your Shield.
What isn't supposed to be happening, for one, is the reset that happens when you swap in a shield amplifier, that would kinda be like an exploit if you ask me, but theres not that much I can do about it, I might look into the Armor Calc script, but as its quite complex I don't know for certain if I can fix the exploit.
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