The most common things I can think would cause this- possibly the patch definitions in-use previously were outdated at the time of scans, you may be using a different patch scan template that includes additional patch types, or there are additional machines in your environment.
We commonly see this type of issue if a new scan template is used (WUScan vs Security Scan). You can view your results in the left drop down list, and compare what scan template was used between the two scans in question:
Also compare how many machines were scanned. If you scan by an IPRange, OU, or Domain, and more machines were available to be scanned between the two, this can impact your total number of patches found missing.
No every scan is scheduled with defaults already set. It would not change. What DOES happen on this machine is in Internet Explorer I lose check in the tick box "Use a proxy server for your LAN". I have a workaround I have used for months which is I have the proxy setting in a reg file on the desktop and I mege it before I deploy. This machine is in a blocked OU with no group policies linked to it. I still have not found out why I lose the setting.
Maybe for some weird reason the proxy setting is now staying put in the overnight scan's? I just thought about this and I will need to verify this. If the setting stays all day then that's the issue. But I don't see how Windows would spontaneosly reset the box if policies are not applying.
You might be on the right track since that may have caused your patch definitions for scanning to be outdated previously.
The patch definitions are by default set to automatically be checked and download newer definitions whenever you run a scan, or you can manually run the download of new definitions from Help > Refresh Files.
Check the assessment and deployment versions by going into Help > About.
Hopefully your proxy settings will stay in place and everything will work as expected from this point on. If you have further trouble with it - might be best to open a case directly with support so we can dig deeper into the issue.