Even in a fan assisted bator the temp will be different at different levels inside it. I didn't realise this until I found out that my hatches were always running late because my thermometer (supplied and fitted to the incubator by the manufacturer) was badly placed, too high above the eggs. It was reading high so I had turned my temp down, and the actual temps at egg level had been a couple of degrees low.
Put both the thermometers at the same level and see what they say. Could be they'll be nearly the same. If one is lying on the floor it's bound to be reading a lower temperature. I set my thermometer so that the bulb bit that measures the temperature is just slightly below the level of the tops of my eggs, which are lying on their sides. That way I know I'm measuring the actual temperature inside the eggs.
What kind of bator do you have anyway?