Changing the keystrokes of a USB keyboard
Solution 1:
The problem you are running into here is that windows is going to recognize your USB keyboard with the HID (Human Interface Driver) and assign it the default/active keyboard mapping that you are using on that system. (Windows and to my knowledge no other desktop OS supports multiple keyboard mappings at the same time.)
Joe's comment of a 72 button mouse might be your ticket. Otherwise, coding out your software to poll the secondary keyboard instead of using the native interrupt signals may work.