Honestly, I've no idea why it's not working. I've yet to be able to test this game in an windows 8.1 environment, however, it seems to work with Windows 10.
The only fix I know might work, would be to run game.exe in compatibility mode for windows xp sp3. To do this, right click on the game.exe icon, and click properties. Go to the compatibility tab (second tab from the left), and click the box that says, "compatibility mode". Set that to Windows XP SP3, and hit okay. Then try to run the game.
If that doesn't work, I dunno what to tell you.
Though, to just be sure, the Audio folder exists in the pokemon pyrite folder, yes?