I don't see why running your fan 24/7 would make your temps go up, that makes me think there is something going on with your heating since your thermostat isn't making up for the difference. You had to have had hot spots since you weren't seeing that till your fan was turned on all the time, fans even out the temps, not raise them. My guess is all that heat was sitting at the top of your incubator since there was no fan to keep it moving. What kind of thermostat are you using? It must be an on/off thermostat which is not a good idea for an incubator, you don't want your temps to fluctuate and that's exactly what you get with an on/off thermostat.
Also, the fan should not create heat, if it does it should be negligible. Computers need the fans to cool them, using a fan that gets hot would fry any computer. Get a nice computer fan, a nice one only costs about $10, and wire it with an old cell phone charger, that will help insure that a smaller amount of energy will be transferred to the fan. And I would never run an incubator without a fan, that is a very bad idea.
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