In addition to shipping the case to the highest court, Jackson also put his interim conduct remedies on hold, a move that pleased both the DOJ and Microsoft. MS was happy for the obvious reason; they don't have to worry about obtaining an injunction to keep the conduct remedies from affecting them within the next couple of months. The DOJ was happy because, had the conduct remedies remained in effect, the Supreme Court would've almost certainly shipped the case back to the Court of Appeals, a venue where the DOJ really doesn't want the case to end up.
The end result seems to be that Jackson delayed short-term gains in hopes of obtaining long-term gains. He apparently figures that there is a much greater likelihood that the Supreme Court will see things his way than the Court of Appeals, so he set aside the conduct remedies to virtually guarantee that the Supreme Court will hear the case.
In short, it seems that Judge Jackson is doing his best to play the system. One analyst called Jackson a "sly fox" and said that "It's interesting to see a judge acting in a strategic matter. There's no other way to explain what he did." Time will tell if his legal maneuvering pays off.