Dumb question -

Are you sure the UltraTemp is set to "HEAT Mode" while the control system is in POOL mode?

I have a MasterTemp gas heater with a Pentair IntelliTouch/EasyTouch control system and I know that the heater settings are separate for each valve mode (POOL vs SPA).

Other than that, I would check all of your temperature sensors (I have two external temperature sensors, one for water temp and one for air temp) and they control the MasterTemp. The only other temperature control would be internal to the heater and it would be a HIGH TEMP cutoff switch that would kick in if the water temperature got too high.

Also, check that you are getting good water pressure/flow into the UltraTemp. It could be that, in SPA mode, you have adequate flow but then the flow is too low in POOL mode.

Hope you find it....hate those little glitches that drive you nuts trying to find them.....as a last resort, you could always call up Pentair Technical Support and they might have some ideas on different points to check.