Did it ever work right?
You have one pump and two zone valves?
Do the thermostats control the pump or the zone valves or the boiler (and the boiler controls the pump)?
There must be some logic to turn on the single pump when either thermostat requests heat and open the specified zone valve. There are many multizone controllers out there and you boiler could have a simple one built-in.
To trouble-shoot this, you need more info on how it is setup.