I don't think it adjusts for inflation. Adjusting for inflation, we have total comp per FTE worker of $49.8k in 1998 and $57k in 2009. But you are right, benefits don't explain the entire increase. Wages went up as well, from $47k to $52k (inflation adjusted).

(Using this inflation calculator: http://www.westegg.com/inflation/infl.cgi)

Also, since the article is about collusion between google and apple, we should really be comparing compensation for the best programmers. I admit, I have no idea whether that went up or not.