It's because it is the pilot episode. I know what I said doesn't really make sense but look at it this way...when they make the pilot they put what money their budget allows into whatever they need to make the episode show as much as they can about the rest of the serries. In the case of this pilot they had to get their hands onto medical equipment, a helicopter to do the outside shots of the hospital, someone to do the medical research for the diagnosis and so on and so forth. All their money went into that stuff, so they didn't put as much money into doing the refinishing and color touch ups. Hence, the weirdness. They really just wanted you to get the general idea, and try to get past the bad appearance.
Pilot episodes are designed to pitch the series to any executives that might be willing to host the series either financially or in some other way. It essentially just outlines the plot of the series and if it looks promising, it might get an order from a network for a couple of episodes. Like Amidon mentioned, since they're only trying to pitch the idea of the series to executives, there is less of an emphasis on making the episode look great (although they can. I suppose they just didn't in the case for the House pilot) and more of an emphasis on simply making the story good and seem appealing. After all, with any financial help that the studio would give if they picked up the series they would make the episodes look at great as they would want to.
It was a new lighting trick they were doing, and some sort of grading. They actually thought it looked good. Then they realized how mesmerizing HL's eyes are, and changed it up to a cooler color scheme.