A couple of things to check.
1. Are you certain that the pumps serve individual zones? Could be both in one universal loop with a valves controlling zones.
2. Do you have a way to check temperature of water into each zone? Like an infrared thermometer. Could be a faulty control valve or even zone thermostat.
3. Do you have a way to check for voltage at pumps both when there's zone demand for heat and also no demand so you could compare? This would determine if problem is in the control system.
FWIW, the system I have in shop runs 2 primary zones off one loop and the pump closest to boiler is always hotter because it's at the front end of loop. Zone valves open and close according to demand.
JLM, that's the first I've heard of BTU determining whether a boiler or water heater. Munchkin terms their 80,000 btu a boiler, but of course it never gets to the temps of old systems, which were actually producing steam, so in that sense it's not a boiler. Most modern condensing "boilers" run temps south of 150°.