Alright, I believe the problem has been solved. Part of it was a group policy issue not being applied the way it should. It's supposed to update every 90 minutes or so, but it doesn't seem to do that. I really didn't want to go from computer to computer to update my group policy so I'll probably just add the gpupdate command in the login script for a night and then take it out the next day. Seems a bit ridiculous to have to do it that way, but whatever, such is the way of Windows I suppose. Thankfully, we can rule out your program as a culprit here! Thank you so much for your help and keep up the good work!
For any others having this issue, please check your group policy results and find a workstation you can do a quick gpupdate /force command on. It worked for me. Red computers are disappearing slowly but surely.