Okay I just tried this again. I left the cooler closed for 15 minutes before I checked it. One of the mice had a tiny bit of blood, and one still showed signs of respiration. So it seems that something is not working right here. I'm thinking the cooler may be too big and/or maybe not airtight enough, or I'm using too much dry ice.

If one mouse is getting too much CO2 too fast and another one 6" away is still showing signs of respiration after 15 minutes, there is definitely a problem. I don't think I should try again until I figure it out. Honestly I never intended to breed this many mice, if any. I certainly don't really want to be torturing them.