Don't be hasty to blame the substrate. I've talked to two large snake breeders that used nothing but Hatchrite this year, and say they will never use anything else again. Blaming the Hatchrite is akin to approaching a vehicle accident, and upon seeing a carrot in the mouth of the rider, presume that the wreck was the result of being under the influence of carotene. Sorry, it was the first analogy that came to mind. The point is, if you used three thermometers per egg clutch, had NO ventilation holes in your containers, used hygrometers to know if it was too wet or too dry, and were certain the sire's sperm was virile, you would have cause for suspecting the substrate was the culprit. In other words, a double-blind study, with sufficient populations of unrelated eggs.
Regarding humidity, it sounds like you had ventilation holes in the container. This is just asking for trouble. I set up egg boxes for over 3,000 eggs this year. I needed to add water to less than ten of those boxes throughout the entire incubation season. NO AIR HOLES. If you like the consistency of the substrate when you set up a box of eggs, why would you risk altering that by letting air IN (and OUT)? As DMong said, you simply "burp" the egg box every few weeks to exchange the air around the eggs. This year, I failed to "burp" about 80 of the egg boxes I set up, and had the exact hatching efficacy that I did with the boxes I did "burp". Mind you, I did not hermetically seal mine as Dmong did. If I had used cellophane (as I successfully have in the past), I would certainly have exchanged the air in the egg boxes at least twice a month during incubation.
I used Hatchrite in a few boxes this year (and last). I was totally satisfied with it. I had to add water to some, but it was because I had opened the bag without completely sealing it between the times I used it.
I just didn't want people to think your problems were the result of using Hatchrite, in the absence of sufficient data of other contributing incubation stumuli.
South Mountain Reptiles