It depends on how your system is piped...it is designed for a primary/secondary loop. That heat exchanger loop is built-in as a primary loop. Unless the flow to the external load is not plumbed properly, that local (internal?) primary loop should work. There are some very specific requirements for the distance between the takeoffs on the primary loop that must be followed or it doesn't work properly. WHen there's a call for heat, most of the heated water should travel through the heating loop, and not just return to the boiler. If yours does, it is not plumbed properly.
The thing would probably tell you why it is shutting down. Is there an error code? If your external heat loops are not done well, the flow may short circuit back to the return, and it could reach max temp and shut off quickly. Otherwise, most of the heat will exit that primary loop and not reach the limit which would shut off the boiler.