In other cars I've had, I've experience a similar problem. Then again, I lived in the midwest, so dead skunks were everywhere...
How bad was the smell? Was it extreme or barely noticeable?
In other cars I found out it was b/c even when you had the A/C on recirculate, a little bit of air was still coming in from outside. That kept the smell perpetuating. Also, if you let too much "stink" get in before switching the A/C to recirculation mode, the stink may stick aroung longer. Lastly, i found that the stink (like that of cigarettes) stays around longer in cooler/colder weather.
If it's still around, try spraying either mild-smelling cologne, body freshener (if that's what it's called), air freshener, or febreeze under the dash on the driver's and passengers side of the Runner while you have the A/C running on re-circulation mode...I found that helps overall and keeps the car fresh for a few days.