Your quite on cue mate! I was about to post about the same thing.
Do you have an ATI card? My ATI HD5650M can run Markarth 30+ FPS no problem but has terrible, terrible unplayble lag and stuttering in Morthal.
Specular effects also seem to hammer my card. At the atronach forge under the College of Winterhold my game basically hangs up.
What's odd is that the game is still running at 30FPS, just lagging terribly.
I'm going to try and roll-back drivers to see if it helps.