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Where did you have your temperature set? I have to run mine at 103 to get 99 at egg level. You're right about humidity - that's pretty easy to keep stable.
How do you know your egg temp is 99? Versus bator temp?
The temp at egg level....I use a Brinsea Spot Check thermometor...super accurate.
I also have a reptile temp guage & reptile humidity guage from Petco in there...also very accurate.
The digital reading on the Reptipro (you can select your set temp) is the temp at the very top of the unit....you set it at whatever it takes to reach desired temps in the middle of the unit which is where the other thermometors come in. Again...this unit has quirks, but they are the best at holding steady temps & humidity with no spikes or drops...you just have to work with it till you figure it out. Once you get it to where it needs to be, you'll have no problems!
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I raise mallards and sometimes they need a little longer. It should at least be 29 days, and sometimes it is 28, sometimes 31. It depends on the temperature in the room where your incubator is. Another issue with fully formed birds not hatching is the humidity. Too much, they will drown in the egg, too little. and they can't get out. I say keep trying.
The best way to take temperatures inside of any incubator is to place a small cup of water at the level where your eggs will be at. Then after the water has sat there overnight check the temp of the water with an accurate probe or mercury thermometer. This will tell you the temp of your eggs as they are mostly water. This is way more accurate than checking air temperature because air quickly separates and moves within the incubator. Whereas the water has a much higher thermal mass and does not have the slight swings that air can have.
This should also prove that the temperature variation from the top to bottom of the ReptiPro 5000 is not as significant as the air temp would lead you to believe.