I can't decide if the habit of referring to Linux as if it weren't a unix OS is the fault of seperatist fanatical linux users, or a plot by Microsoft to make it appear that Windows NT has captured the server market.

Probably both. MSNBC reports that in 1999 NT had 38.1% of the server market, while Linux had 24.6% and unix 15.3%. Note that if you add the last two numbers, the result is greater than the NT percentage.