Do medium-large fluorescent light fixtures in a small room (light is 3
feet above the persons head while standing) have any effect on a
worker in that room if they are under it 12-16 hours straight?

This sounds like a very common work environment, one so common that
any negative effects of the lighting would have become well known.  Of
course, there are always persons who complain, and maybe some who
suffer demonstrable effects from working in such conditions, but the
continuing use of such lighting suggests that general negative effects
are unproven.

What effects do you have in mind?

Without a shred of scientific evidence I can tell you that the
scenario you describe used to give me headaches by the end of the day.
The solution was to pull the starter out of the light fitting so that
the tubes above me did not come on. Of course this resulted in a 2
year game between the maintenance man and I during which I ended up
with 50 starters but no more headaches

Ah I see, thanks for replies. Well Personally I read that the refresh
rates for this lighting has gotten a lot better. However, I can still
see the refresh rates, even with the newest flourescents. My eyes are
just well tuned I guess. Since I can still see them if I am not
focusing on something else, I was wondering if it can cause some
underlying problems from being under a light for long periods of time.

They always caused me migrains as a child and I have often wondered if
they might trigger epeleptic fits if not cause epilepsy . Why not
accidentally rip it off the ceiling and replace it with a light bulb
on the maitenance man's day off ?

I heard that is possible, and as for the ripping it out.. its my small
office and its to save money :) ... a lot cheaper vs a ton of 100w
bulbs :)