I googled the fungus gnat and the pictures I found make it seem like it isn't a fungus gnat. The ones we have aren't angular bodied, more rounded. I wish I could get a good picture of them, but they are just too tiny! On CSU's info page about fungus gnats, it says that they take 2-3 weeks to go through their larval stage, but we have only had the cups active for the past 10 days or so, so I'm not sure if that's even enough time to produce adult flies. Prior to that, the soil cups were not being watered and they were allowed to dry out for about a month. So that timing just seems strange to me!
The soil isn't kept damp either, we only water them once every day or every other day depending upon how the plants are looking. They are in an air conditioned bedroom, so it's pretty dry inside and the water evaporates from the surface of the soil ~4-6 hours after it's applied. I wish we could move the cups outside, but we have about 500 of them, so that would be impossible!
I don't have any gnatrol hanging around, but we do have another brand of BT. I just don't want to use anything unnecessarily as it appears they aren't affecting the plants at all. Everyone is still happily sprouting along! Perhaps I will take some pictures in a bit, we have some great looking beans and cucumbers that are starting to get huge as well as some itty bitty peppers.