It appears, to me at least, that the Heavy Ammo Bug fix didn't fix it for machine guns, specifically at least my Super Good Advice. I have 200 rounds when I go to orbit, and when I land again I only have 139. Same with Thunderlord...181, then go to orbit and come back and I have 180. Gjallarhorn has 7 before and 5 after coming back from orbit.
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Going to orbit and back to the game world makes you lose ammo. This is intentional.