It sounds like you may be confusing the "common use" heading in the documentation for fixed functions. There is no specific "pause" function in the hardware, rather recommended uses for the buttons. The "pause' button is simply "Button 18" on the device, so changing them around doesn't cause any issues. If you go into the Windows Game Controllers test, you can see what the hardware is doing, and verify that all of the functions of the GP-Wiz40 are working. However, it sounds like the MAME
variant you are using may not be properly saving control configurations, or causing them to change. Have you tried a different version, or perhaps the official MAME release to see if the issue goes away?
Also, make sure that you don't have separate configurations defined for the game(s) you are seeing this happen with. If you do, they will override the defaults. If you had game-specific configurations defined for your gamepads, those definitions may be linked to something which no longer exists. Try clearing any and all game-specific configurations and see if the issue persists. If all else fails, start from a clean slate to be sure.
As for the Mac OS, we do not directly support it, so I cannot speak to what the issues are with that OS. I know from doing some research on gaming controllers and Macs that they seem to be picky about the hardware they work with. I have seen reports of game controllers locking up the system, and other strange behavior, in the absence of drivers, or in cases where the hardware was not specifically designed for the Mac OS. The software you downloaded is reading the reports correctly, but the application you are running does not seem to be interpreting that data properly. You may want to check with the author to see if this is a known issue. Alternatively, you might want to try
ControllerMate to see if it allows for calibration of the axes. Frankly, it seems odd that the OS doesn't have a built in function for gaming controller calibration. Are you certain none exists? Alternatively, you can use any 4 button inputs for joystick directions (provided the application allows for it... most do) in the event that that you cannot calibrate the axes. With 40 inputs, you will still have enough to disregard the axes and make a fully functional 2-player panel, with some left over.