See that in device selection window "Show all targets" is selected.
Check that the kitprog is in "Mass storage mode". Check Kitprog manual how to get out of that (Pressing 'reset' for more than 10s).
This was the case for the majority of them, I was able to get those ones back out of mass storage mode easily. Unfortunately, the last 3 are not in mass storage mode. I can put them into it and take them back out, but that isn't the issue. Show all targets is selected within the device selection window. Any other ideas on what it could be? They may actually be bad, the students in this course make their own custom boards using Cadence and we mill them out right here at school. So its completely possible that something within their boards fried the chips, but I'm just not sure these ones are actually bad. Most the ones that are bad seem to have GND shorted to VDD or a Pin is shorted to GND or VDD. I have found most of these due to the board getting really hot or the status LED on the main board will turn off. These appear to be working (at least none of the symptoms above) I just can't see them in the device selection window, it only shows the kitprog/serial number.