Where are you measuring the temps?
I have an older GQF cabinet 'bator. I have a digital thermometer in the hatching tray at the bottom, and a magnetic thermometer on the front of the top turner frame. I also use the metal thermometer that goes through the wall of the 'bator near the top. Each of my hatching trays has a metal thermometer (the kind that look like meat thermometers) in the center.
My temps are less than .3 degrees difference.
Do you have a clear window, or are you opening the door to the 'bator to read the temps?
I have a clear door on mine, so I can check all temps without opening the door.
Is something obstructing airflow from the fan? If there is something blocking the fan from circulating the warm air, that could cause a temp difference.
The only time I notice a significant difference in temp & humidity is when I have eggs hatching in the hatching tray at the bottom.