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Earlier this year, I realized that there were several thermometers here & they read different, didn't know which one to trust. So, I ordered 2 glass thermometers, inserted into "water wigglers" & found them both to be exactly the same & use them to judge accurate. They were ordered online along with 2
Brinsea Spot Check digital/probe ones which read the same as the glass ones. I used the water wigglers to judge the interior temp of the egg. Finally, I had temps that I could trust to read 99.5 for a fan/forced air incubator. See page 1, post #1 for homemade wigglers with a ziploc bag & glass thermometer. Also, using the wiggler/glass thermometer as an accurate #, I was able to adjust the small thin "lay it on top of the eggs" one by slidding & adhearing it in the accurate position.
My last incubation in May hatched on time, instead of the usual day late that I'm used to; with good hatch results. Although the 3 fertile eggs started hatchingd on time, I realized by watching my old digital therm that the temps had run nearly degree higher; in addition, I did not have an easy hatch as before at a slightly lower temp. Everyone must "get to know their equipment" & find what temps & humidity works best. I will run my next incubation a 1/2 to 1 degree lower.
As for what you are describing, do you have a fan/forced air or still air incubator? Are you using a glass thermometer in water or a water tube? Yes, with lower temps the hatch seems delayed & with much lower temps so can the development be with poor results. I trust the glass liquid filled thermometers over digitals.
Happy hatching!