Same issue here, using a 5970. Thought at first it might be a multi gpu thing, but apparently not. It only happens in first person though, third person isn't affected at all strangely enough. And also only if you use fullscreen, windowed is fine.
It can happen outside as well. It's really weird, my fps are locked at 60 (v-sync) when this happens, there's no framedrop at all.
Here are some other threads on the same issue:
http://hardforum.com/showthread.php?t=1653449
http://www.tomshardware.co.uk/forum/115099-25-skyrim-stuttering-firstperson-view
Some suggested using windowed mode all the time with that borderless windowed mod. But that didn't help stability or performance here.
Others said to use a FPS limiter, and while those do fix the issue they introduce some drop in performance.
Hope this gets sorted out by bethesda cause it's pretty annoying
