I had set the dip switch (#7 I think) to the wrong position. So it was set to "continuous space heating" I wrongly believed this setting would cause the unit to operate only when it sensed water flow caused by the secondary circulating pumps. Though it did fire when the circulating pumps were turned on by the thermostat, the primary (internal) pump was trying to provide continuous heated water all the time. So when this happened and the secondary pumps were not cycling water, it was shutting the burner off then resetting because the high temp setting was being reached.
I initially had my thermostat wired into a relay and then from the relay into the secondary circulator pumps. I had no wiring connected to the navien. I have since ran my thermostat wire directly to my navien. I still need to do some reading on the wiring side to figure out the correct way to connect the relay to the navien. I currently just piggybacked some jumpers to the relay to activate both the navien and my circulator pump at the same time. This is fine for the single zone but will not work for two zones operating on two thermostats. Again, more reading/learning. Thanks for the replies.
By the way bannerman, I was thinking the same as you before I turned to posting here. I watched the temps on the info screen and none of them were ever the same when the unit would start up nor did they ever reach a cold enough temp to start the freeze protection. I was certain that would be the issue. Thanks for the suggestions