Not sure if it's 1-to-1 the same problem I had, but when using a Win98SE virtual machine to play FF7 on a laptop, the keyboard controls would revert back to their installation defaults *ONLY* on character naming screens. In order to proceed, I had to hold down the Fn button to make the keyboard operate on the keypad-ish secondary meanings, name the characters, and I'd be back to my customized controls.