Complaints like this are not uncommon. Very few buildings are used in the manner that they were originally intended. The causes are varied like the company rapidly changing in size, a new tenant occupying the space, remodeling, etc.

Regardless of the reason, the problem can be solved with the use of a zoning system. Where you might have had one thermostat before you now can have multiple zones and temperature sensors with one central control on the same system.

After properly calculating the demand for heating and cooling for each space (it does not have to be an enclosed room) the supply runs can be properly sized to supply the right amount of air. Then thermostatic controlled zones can be set up so the right amount of cool or warm air can be distributed as you want.

We have seen some buildings go from more than a 10 degree temperature difference from one area to the next to less that one degree variance.