Were the seeds all of the same variety? Sometimes, seeds just germinate at different rates, for no reason at all. In your situation, before considering air circulation, I would look first to the heat source. Possibly your heat mat is hotter either in the center or around the perimeter, thus causing better germination either in the cooler or hotter areas. I have seen this before using my cheap heating pad, as the coil inside makes certain areas of the pad hotter than others. Air circulation really is only important during germination to the extent that you don't want the seeds to rot or develop a mold/fungus. If the un-germinated seeds aren't rotten or severely moldy, then air circulation is fine, IMHO.

The tray had 1/8" water in the bottom to help insure even temp across the flat. All the seeds were from the same packet. The dome was "down" on the flat and humidity droplets were on the lid around the outer 1 1/2" of the lid. The center was "dry" due to heat from the lamp I assume.
Dave

Ok, since you say 'dry' in quotes like that, I assume you mean...not dry? Just comparatively drier than the outer cells? Assuming you started with seed starting mix that you thoroughly wet and then squeezed the excess water out of before filling the cells.

I've always had really good luck starting peppers (nearly 100% germination). I use a heat mat and a humidity dome, but I always prop the dome open a bit to let air circulate. I keep them dark until the first seeds begin to germinate, then I take them off the heat mat and put them under lights. It can take a while for stragglers to catch up, so be patient. I had one variety (Yolo Wonder, I think) take almost double the time of the others I planted. But even they eventually sprouted.