The RA89A in your case is working as a isloation relay for the upstairs. It allows the upstairs thermostat to be connected to the L8124 aquastat on the boiler or activates the pump by going through the RA89A so the circuits are separate/isloated from each other so as to not cause or allow interference between the two circuits. Now with all the part numbers the game of figuring out the problem is much simpler.
Since the upstairs section is running all the time the RA89A more than likely has its contacts stuck or is energised all the time by the thermostat. See diagram below.
http://customer.honeywell.com/techli...s/69-0791b.pdf
See figure 2 on the wiring diagram to test.
Remove one of the thermostat wires off one of the (T) terminals. This is where the thermostat hooks to the control, Both T T terminals are for the thermostat but by removing one wire it will drop the RA89A controler out of the circuit and stop the call for heat from being sent to the L8124 main boiler aquastat. You should here a audible clicking sound as you remove the wire with the power on. This is caused by the relay inside the RA89A kicking on and off quickly since during the T wire removal there will be times during removal that the circuit will be made or broken. If you do not hear the clicking then once the wire is removed touch it back on the T terminal you removed it from and then you will definitely hear the clicking.
If you do not hear the clicking as described above then the relay is stuck or electrically burnt closed. The next test will prove that point.
Go back to the figure number 2 in the honeywell instructions and find terminal number 4. This terminal is one of two that controls the load. The load signal is what actually activates the boiler or pump as a signal that the upstairs wants heat. This time turn the power OFF then disconnect the wire from number 4 terminal and put a piece of tape on the wire so as to prevent it from shorting out on a back feed condition. With the number 4 wire disconnected there should be no way the upstairs thermostat can call for heat or cause the boiler to activate.
This simple test will prove weather or not the thermostat or thermostat wire is causing the problem upstairs or if the controler RA89A for the upstairs heat is causing the problem.
NOTE: When there is a call for upstairs heat and as the circulator comes on to satisfy that call for heat the boiler may activate at sometime durning that call for heat. The reason is that the boilers temperature will drop as heat is sent upstairs and naturally the boiler will want to heat the water back up to maintain the preset boiler temperature.
Post back with results.