How did the outside of the packages look? Every box of shipped eggs I've received had bright, fluorescent green, yellow, or pink stickers saying hatching eggs, I'm alive, do not X ray on them.
I've read on here about someone mentioning postal "dead zones" before. Basically they hatched shipped eggs from the same seller several times with good results then the moved to a different state. When they ordered eggs from the same supplier at their new home they had horrible hatch rates. They blamed it on the shipping service. Just what I read but seems likely.
I've had a very good shipped egg experience so far. I can't comment on chicken eggs but out of roughly 500 shipped quail eggs from three different suppliers I have averaged a 74% hatch rate on all eggs set and a 93% hatch rate on viable eggs at lockdown. My worst hatch was 62% on total eggs set and 86% on viable eggs at lockdown.
You also want to rule out your incubator as a possible reason for poor hatch rates. Buying a separate thermometer/hygrometer and testing its accuracy is extremely important in successful hatches. Obviously if you're getting great hatch rates with local eggs the incubator is probably not the problem...