If you didn't look in the Forum Problems/Errors forum up top, the promotion the old ad banners were on ran out, the staff is working on a new ad promotion that should put us back with just content related ads any time now. I forget who noticed, had Adblock on, but NoScript apparently didn't work, so he got the popup from a blocked ad he couldn't see..............last couple of days, I've seen the Motherboards.org logo at the top of the page fairly frequently.
But yes, the ad banner at the top of the page has been there at least as long as I have, more than a year. Pretty much always been there, as far as I know. Half the main page is ads, too.