Elite Four members don't give correct reward money with Amulet Coin?

Solution 1:

What's happening here is that you are dying after you defeat the first member of the elite four, which halves your total money. Since you weren't checking your money between defeating the first member and losing to the second member, it appeared that you were getting half as much money as you really were, since you immediately lose half of all the money you get.

Solution 2:

OP's answer from the question:

According to Bulbapedia - "Before Generation IV, half of the money on hand was lost and this loss was not explicitly stated to the player."

A little bit of research goes a long way. I didn't quite know what to look up before asking this question, and what I did look up returned nothing useful. But that link provides quite a lot of useful information indeed!

Thanks @Frank for helping me along the way!