Is it still air or forced air? Do you have fan in the incubator? if you do, it's forced air. The temp requirements are different. 99.5-100F is for forced air, at the middle of the eggs. Actually, with forced air, the temp should be pretty even, there shouldn't be much difference between top and bottom. But still air is 102.5F at the top of the eggs. The bottom will be cooler. I don't know for sure how much cooler. The temperature will be different in different layers. Cooler at the bottom, warmer at the top.
Why can't you put some small item, like a small plastic box or an end cut off of an egg carton, and set the thermometer on that to bring it up to egg-top level? I saw on another thread you said you have to put the thermometer on the bottom, and I don't understand why you can't do one of the things other people do? You could cut a piece of cardboard from a shoe box and lay it across some of the eggs, or before you set the eggs, on top of some egg-height size something, and put the thermometer on that to check the top temp. Then, once you know that's right, you could lay it on the bottom, let the temp stabilize again, and see what that reads. Then you'd know what temp you need to keep the bottom.
Can you post a pic of the thermometer? Does it have a probe on a wire, like most? Can you tape it to a plastic Easter egg and place the egg in with the real ones? you could stick a blob of clay or tape a rock to the inside so one side will stay down, and the therm stay on the top. there are kinds of ways you could place the therm at egg top level. I'm sure there are scores of ways to do it this.
Why not post a question about how to place the thermometer at the correct level?
BTW, do you have a liquid or mercury type thermometer at all? The digitals are sometimes not very accurate. I have one that reads all over the place, I quit using it and stick to the liquid one. One of the ones with the red stuff in it. (I think they're tinted alcohol.) I checked the liquid one by putting a regular mercury fever thermometer in to see what it came to. Those stay won't go back down by themselves, you hae to shake them down, so they're no good for monitoring, but to see if your others are accurate, they're pretty good.