Bumping this since mods locked the other thread about getting better results from automatic navmesh generation. (This is not about "The Navmesh Bug". It's about using the CK to better effect.)
As an addendum to the first post, I did run into some problems where Havok extended the navmesh through pillars where NPCs would get stuck, but fixing it was just a matter of plopping down a few new nodes. Much easier than hand building where recast generation refused to extend navmesh anywhere in the vicinity of the pillars. Or half the landscape.
Setting "overlap distance" in the Havok dialog to 256.0 seems to produce cleaner results as well. I'm not sure why this is, but it seems to be a somewhat magic number, as 128 and 300 resembled each other more than either of them resembled 256.