I'm having the same issue on an i5 2500k and GTX 680. Was running fine for ~20 hours at a steady 60fps.
After saving Wulfram I went back to explore the house I found him in and noticed the framerate was dropping. I saved, quit, started Fraps and reloaded. Fraps reported the fps as 25 which was lower than I'd ever seen. As I continued to play that file, the fps dropped to 12, and then to 8.
And that framerate 'sticks' in the save, meaning wherever you go it persists, in small underground areas, in the city, in the pocket plane - everywhere. Flipping graphics options on and off doesn't fix anything. I'd been running the game V-Synced and Triple Buffered through D3D Overrider and I shut that down and loaded without it, didn't see any difference, just screen tearing with sub 15 fps.
Backing up to earlier saves restores the fps to 60, and I'm going to try and continue from an earlier point to see if the problem reoccurs.
I've emailed support with a .zip containing two saves, one with an afflicted fps and the other without, just like mformule.
That is the exact problem I'm facing, except the problem reoccurred at the same location.
