Always something more to learn and tweak with the homemade incubators. Sounds like you can find a solution now that you defined the problem. I have high air flow at 2 locations and try to reduce direct air flow; I move the eggs around a lot so they have equal opportunity to get a blast of air. ANd just now, eureka! I hit a solution to try in my Henny PEnny.
I've been saying for a while now that the fan can cause problems in hatching chicks.. I just wish the incubator manufacturers would pay attention and fix their darn bators (an on/off switch for that fan which blows directly on the eggs would be a major plus and they could still have a circulating air fan in the bator.. just not have it blowing directly on the eggs)