This problem will no longer occur once construction is completed. Since the VAV units respond to local situations, two units may be running at different rates because the two areas get more or less air circulation through open doors and other factors. This is the whole point of having a local sensor, so that each area has an independent air flow to adjust to local conditions. The fan coil window units are the main cooling and heating for the area. The function of the overhead in these areas is to supply outside air and allow for required air exchanges.
Temperature control is managed through the window units, which have individual temperature controls.
If the window units are turned off, the area will become stuffy and the temperature can rise. If windows are open, they introduce untreated air into the system and let out the conditioned air to the outdoors. Controlling temperature and humidity is not possible when this happens because the untreated air reaches the sensors and they try to over-compensate for the untreated air. If a window is open at one end of the room, it throws off the sensors for the entire room. It can also draw in fumes from the street.