The i-pac does not work properly with those ps/2-usb adapters, and the advice I've been given is they only function correctly in USB mode if using the proper PS/2 to USB cable supplied by Ultimarc. With the adapter you have the PC is recognising it as a USB device fine when you run the games, with the default flashed key config, whilst the Winipac utility is looking for a specific i-pac signal, which it is not picking up correctly using your connector. This could be why it's not 'holding' the key config you are programming even though it says it is.
Why is it essential to run your ipac through a USB port? The native PS/2 connection is a lot more reliable and straight forward and avoids any of these complications as there should be no conflicts going on (a keyboard port is just that, unlike a USB port). There are no benefits to having it through USB.
If you really must have it through USB I'd e-mail Andy at Ultimarc.