My boiler won't come on when I raise the upstairs thermostat, but will come on when I raise the downstairs thermostat.

You have control problems. The system controls can contain many different parts and be wired many different ways. If you have a meter and the knowledge to use it then you can troubleshoot your system. If not then I suggest you call for ON SITE SERVICE since these type of systems are specialized for each type of install. Further damage can be caused by trying to repair your controls without on site help from a professional. Sorry but there are just to many ways these systems can be hooked up and I would not want to give you bad information and cause further problems.