Is it possible you're just getting into larger battles now than you have in the past? The more spells and such onscreen, the more load it puts on your GPU. Also if you have dynamic skies on and there are windows nearby (or your are outside), that will hurt your performance, too. With a gaming GPU it should be no problem whatsoever (I almost never get fewer than 90fps in my uncapped dev builds on my five year old 8800 GTS, with dynamic skies on), but depending on your GPU you might really want to use static skies to make sure that you can get a consistent 60fps.
Or it's possible there's some new issue that I'm just not seeing, of course, but this is the first I've heard of it. It could also be that eagle bug where the monsters are stacking up consciousness shards to a crazy degree. That's new in this version and would cause massive slowdown with eagles present in exterior areas, but it wouldn't be something you'd see indoors or with smaller numbers of enemies in most cases.