What was quite amusing was that over the 5 years Microsoft would stop supporting Win2K server, so you would have an enforced upgrade of OS, and possibly hardware, on the Windows side around halfway through, and this wasn't taken into consideration. This extra cost would have completely turned the results of the study around on its own.
Also Linux/Unix sysadmins can administer 50% more servers than Windows sysadmins due to the nature of the OS, although they cost around 10% more to hire. This wasn't taken into consideration either.
There was a follow-up on the Register regarding this "study".