Stuck on "listing ids of missing updates" after reboot

When I run the program, it does some initial updates, and then reboots the machine. Then, I get a window I need to click either "okay" or "Allow" on to resume the update script (Never had to do that before) and then it gets stuck on "listing IDs of missing updates" and it sits there. If I reboot the machine, the box keeps coming up confirming I want to run the script. When I cancel it to do the updates manually, it searches for updates endlessly. Whats the issue?