Some thoughts...
If the were in fact fertile, and large fat white eggs usually are, then it IS most likely a husbandry issue on your end. Occasionally an good egg will die naturally on its own, but to have two die naturally would make me think something is going on.
Without seeing them, its kind of hard to diagnose, but If I had to guess as to a cause...well, read on (I'm assuming your temps have been stable throughout)-
In my experience, most egg death can be attributed to overly wet conditions (why I devloped my modified no substrate method). If they were overly dry, they would start to collapse or dimple prematurely. Since you didn't mention them collapsing, I would lean toward overly wet substrate. I think I recall you used vermiculite. It should just clump when you squeeze it. If you can actually squeeze water out if it, it is too wet. Its kind of hard to swithc up midstream, especially since you have one small incubator, but I would try to set up another, dryer egg box (or better yet, go no-sub). The new eggbox with dryer substrate should have less ventilation, to ensure high humidity.
If you think that the moisture in the substrate is at an appropriate level, then I don't know what else to suggest. Keep us posted...