Both feeders should be feeding the same.
Did you just plug it and start using it? whats the FEED RATE (FR)? if it's says 99 then both stokers should run a lot and the blowers will be running full. If so, turn your setpoint down below room temp. IT takes time to react, it might take a few hours for it to stabilize again and get back on track.
Almost sounds like you have something wired wrong, check the cabling, check the Thermostat cable too, unplug and plug everything back in. something might be loose or dirty. Have you powered it down, unplug the control box, and replug everything back in, i know you;ll have reset date and time.