I have found that the size of the egg container plays little to no importance (unless of course, you're using a container that is clearly "cramped". More important is humidity in this case (the reason your eggs were dimpling so early on) and air flow. Early on in the incubation process, eggs do not "breathe" much, so swapping out air in the container is not as important as it is when you are two weeks from hatching and the eggs begin to dimple, allowing more oxygen into the egg.
I use Rubbermaids shoebox bins for my clutches (sometimes two clutches) and they hold 840 cu. inches of air. I half that (420 cu. inches of air) by using 50% of that space for medium (Perlite/Vermiculite with enough moisture to attain and maintain 100% humidity), my eggs never dimple early.

Seems your issue was not the size of your egg container as much as it was maintaining a proper humidity level.
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