We have the same situation here. DS8 (3rd grade) could never sit still from preschool through 1st grade. He had an awful time in second grade with a teacher who was very much like a drill sergeant.
Like previous posters, DS can easily be still when he's completely engaged in something. In fact, when he's really into a book, you could mistake him for a piece of furniture because he's so still for so long. *lol* But with things that he's either not challenged with or not completely engaged in, we've found that he actually is able to focus better when he's moving around. The psychologist who did his IQ/achievement tests noted it during testing, too. Movie night used to be a hoot around here -- DS might be upside down, doing somersaults on the couch, or bouncing around the room while he watched, but he could tell you everything about the movie.
Personally, I wouldn't worry about it. It has definitely gotten better for DS over the past few years. He can control his need to move much better and for longer periods. I've looked at it like his brain is craving stimulation -- and if it's not getting mental stimulation, it seeks physical. Maybe it's true of all the kids, but for most the threshold for the mental stimulation required is lower.
And if your DS's teacher is willing to be flexible and let him sit on a chair and that works, that seems great to me. It's nice that she's been able to find a workable solution.
