If I correctly understand your problem, your converters are connected in parallel for powering their own load and you are measuring the differential potential between the ground of your non isolated converter and the primary ground of the isolated converter ?
How do you do your measurement ? With an oscilloscope or with a multimeter ? I think you are trying to measure the average voltage across the capacitor between the primary and the secondary of your transformer of your isolated converter.
--------------------------E D I T --------------------------
As you can see you are trying to measure the voltage across your transformer isolation, ie the potential difference between the primary ground and the secondary ground.