Looking at the game and the new technology that's come out for new systems, I think they custom-crafted a physics system into the game engine, instead of trying to comply to the restrictions of a stand-alone physics engine. It would give them the total freedom that's required in a game of this caliber. Its what I would expect.
I'm pretty sure they're still using havok. Like they mentioned they were now also using havok's animation thing? Though I don't think Oblivion's and Fallout 3's terribly imprecise physics were havok's fault so much as whoever implemented it, so I think a Bethesda-made physics engine would be even worse.
You could take both roads and say that Bethesda did a very poor job of using an outside physics engine in ways that were good for their game, and now that they've made their own it'll have all of, and only, the features they need. Plus they'd know how to actually use it.
I haven't done much research, but it looks like FO3 did indeed use Havok, but the logo is not on the box art. So, it's still in Skyrim?
Yeah.Havok Behavior (Animation)
Bethesda is again returning to the Havok system. Beyond just the usual physics people usually associate with Havok, Skyrim will be using Havok's new "Behavior" system, which allows for improved and more easily designed animations.
They are indeed still using Havok, the logo just isn't on the box any more. The wording I emboldened makes it sound like they're doing animation as well as physics with it.