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I read through the whole thread, and nobody questioned the integrity of your thermometer.
Get 2 or better 3 decent quality thermometers preferably one digital among them and compare readings.
I know an experienced poultry breeder who entrusted his single thermometer and lost a batch of vary rare and veeery expensive eggs, I won't mention the breed, cause some of you could freak out. (I almost did)
Anyway he found that his "thermometer" was 7 degrees Fahrenhite off.
I have been jumping through hoops with my thermometers as well.
One was reading 100.2 while the other read 97. I thought I was having trouble getting an even temp in the bator and after messing with it for over 24 hours I decided to trade places between the two thermometers but the same one was still reading higher but now it was on the other side of the box.
I threw in a 3rd (They are all digital) and picked the best 2 out of 3. Now all is well.