That's right, as master you see all accounts listed, but secondary don't see the master one. So they can never get it to login with, not unless given to them or accidentally post it in system chat. Wasn't sure now what access secondary have on base to do, but after what you said. Yes, could well be the base has a secondary account he's unaware off being used, he needs to check base accounts and see what is listed.
He doesn't say if he's running the base on his own, or if there's others involved using secondary base accounts. If there ARE others involved using base accounts, then after what "SummerMcLovin" said, you'd have to suspect you may have a rouge base member onboard. But more importantly thinking about it as well. Did he actually build this base himself? Because if he didn't, then he might not be using master pass after all, the original base builder may have it with full base access. He won't know that, because all he'll see listed is just his secondary base account, he'll not see a master one listed.