You need to calibrate one of your thermometers. Do you have a digital fever thermometer? Those are guaranteed accurate to +/- .2*F. I use either a digital or my old stand by: an old fashioned mercury bulb rectal thermometer. Place the gold standard in a cup or bowl of water that is approximately 100*F, along with the submersible thermometer you want to calibrate. Don't let either thermometer touch bottom or sides of the container. Wait for them to equalize, then make note of the difference. Say your medical grade thermometer reads 101.2* and your other one reads 99.7. You then know that your other one reads 1.5* LOW. So, add 1.5 to what ever reading that gives you to know what the temp is in your bator.
If your bator has a fan, your goal should be 99.5*. If no fan, the reading at the top of the eggs should be 102*. Before putting eggs in the bator, run it for a few days, checking all areas of bator for warm/cool spots.