It could have something to do with the indoor air quality (search for 'Sick building syndrome: http://en.wikipedia.org/wiki/Sick_building_syndrome). I've worked in an environment where the air quality was lacking, and I always felt horrible after a couple of hours. Do keep in mind that in a packed office, with multiple computers, printers et al the CO2 levels will skyrocket.

Ventilation is important, as is cleanliness and excersise. If the problems persist, look out for a bigger office!