I did some testing.
Initially I thought I was able to reproduce the problem, but it turned out to be false alarm. Yesterday I cleared my programs shortly after I ran an update in GUI mode. Then I schedule my automatic update at a time shortly after that. Automatic update failed, but only because mc2xml detected that it was run shortly before, so it simply returned without further action ("no new data available").
So I waited until today. Cleared EPG programs again. Scheduled an update at 9:00 am. Update worked. This was done on two machines, a Windows 10 and a Windows 7.
For those of you who are doing some testing, do not expect automatic update to succeed shortly after you run a manual update. If you run repeated manual updates, each time it will end up succeeding, but each time you will be asked to enter your location and provider info.
Run a manual update. Make sure automatic update is turned on, and the automatic update time is set properly. Then you can check to see if update succeeds the next day. If it does not, then we need to investigate further.