I'm not sure how to tell if they were malpositioned, but they were not internally pipped as I had to break the membrane. I will say when I candled at lock down, I did think one was in a funny position as the air cell was kind of crooked, meaning not totally on the large end. I definitely saw movement on more than 6...more like 12. The air cells were dry, but there seemed to be fluid within the membrane...which I don't think is normal. It stayed about 40% or just under for the 1st 18 days...it did drop to about 15% twice, but only for a few hours each time. The last 3 days, it averaged 60%...just couldn't keep it at 65%. Does that help? A few friends have asked me to incubate for them, so I really want to understand this before committing.
The drawing down of the air cell that I think you're describing is actually supposed to happen. This is one of the early signs that the chick is getting ready to hatch. If there was a lot of sticky fluid where the chicks were this is something called "sticky chicks" that can be caused from too high of humidity during the early days of incubation. It prevents the chicks from being able to rotate properly to pip. There seems to be a higher likelihood of this happening with shipped eggs as well but I'm not entirely sure why.
I can't remember if you already said, but what incubator are you using and are you using a secondary calibrated thermometer and hygrometer?