Are We Talking About the Same Thing?

Most people assume that FOX News channel is a very conservative network, or at least that their regular pundits...I mean hosts are very conservative.
So when I saw this on ABCNews (here: http://abcnews.go.com/Politics/wireStory?id=1338898), it seemed odd, but not surprising. Over the last election, FOX tried to put out a "documentary" that was critical of Kerry. The reason behind not showing an ad, which was against the Alito nomination, was that it was inaccurate.
But then, I went over Factcheck, which had an article on an ad that was against the Alito nomination (here: http://www.factcheck.org/article360.html). Their assessment: the ad was true as far as the subject matter that it covered.
So here's my question: are these ads the same commercial? Because if it is so, then FOX would have much more to worry about. Such a move shows obvious discrimination. And of what I read, these are the same commercials.
This isn't a decision of the FOX News content managers, it would be of their advertising department. Usually, to avoid problems in associating the content with the paying advertisers, media companies keep the two departments seperate. So why would FOX News do such a move? It certainly not because of the ad's inaccuracies.