@h2oratt Good Post!
I can't answer the question because I need to know:
1. What is the incubator?
2. What thermometers are you using? Many are Crapp!
3. I do not know what the tray levels is about.
I suspect the answer is to either get a new incubator, assuming that the temps are correct or contact customer support for the incubator you have.
Vents could be a problem or it could be a poorly built home made incubator? If a home incubator, the fan is not installed correctly or insulation is sketchy.
It the temps are really that far off, you would have to rotate the eggs a lot or use only the part of the incubator that heats the eggs to 99.5 degrees F.