"but the key was that the hardware was different, the software was an entirely different methodology, and the more modern software could not be loaded onto the older example and be run without error."

This is just RIDICULOUS. By this line of thought, every time new hardware or software methodologies come out, you could patent the same old software solutions again!

If reimplementing a well known feature, algorithm, or whatever on new hardware isn't obvious "for a practitioner skilled in the art", then I really don't know what is.