This is all because in a still air incubator, the air stratifies and layers out. Heat rises. If you don't have a fan circulating the air, then you're going to have different temperatures everywhere.
So, people have figured out that to get the inside of the egg 99.5, that takes an air temperature of about 102 at floor level. And, they've figured out that if the air is 101.5 at the level of the top of the eggs, then at the level of the center of the egg it's about 99.5-100.
That's a bunch of trouble, isn't it?
So make a water wiggler and slip the thermometer in there, and put it on level with the eggs.
You can get a thermometer with a probe in the cooking aisle at
Walmart, if you don't have one. Calibrate it by packing a glass as full of ice as you can, then putting cold water over it. Put your probe (no, not that one, the one attached to the thermometer, silly!) in the glass and stir it up. Watch the readout until it quits dropping. It should go down to 32*. If it's one side or the other, then remember that you have to always make that adjustment when you look at the readout from now on - so if it reads 28*, you're going to have to always add 4* to the readout, and you'll want to be shooting for that readout to say 95-96* instead of 99-100*. Make sense?
Then double-bag a cup or so of water in ziplocs, roll them in a tube and run masking tape around them to hold them there, and slip the probe through one of your ventilation holes and into the center tunnel of the bag. Voila! Water wiggler, and a good solid estimate of the actual temperature inside your eggs, where it matters, instead of the temperature of the air around your eggs.
That water's going to help as a heat-sink, too, to steady your temperatures some. Good luck!
