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I'd have to agree. The carton method might be your problem. Air in the still air is very stratified so temp of the higher up eggs is varying alot from the lower down eggs. I'd just lay them on the wire and turn by hand at least 3x a day. Don't give up on the 4 you have. I've got a LG still air and it took me awhile but I finally got it and now have 13 babies now 3 and 4 weeks old! - ya I too ended up with staggered hatches. Also I kept my temp 101- 102. I had 2 accurites in there(both reading 2 different temps) Just kinda averaging the temps between them. These were standing upright but the temp should be taken at the top of the egg. Hang in there and Good Luck!
You could also use a sponge for the humidity, and just tilt the bator 3 times a day. I believe the problem is with the heat source, not the rising heat. just my opinion.