I can tell you for certain,
I've always had automator in system tray, and I've always had both boxes checked.
The only thing I can think of is that normally I quit automator from the system tray before running the AC backup (since scheduling backups turns on automator anyway). THIS time, as you said, I ran AC backup (and "schedule") with automator running in the tray.
The other difference: normally once I go to the trouble of running AC backup, I do a "backup now", whereas this time I ran the "schedule backups" in AC backup and closed out without backing up "now."
So the solution must be in one of those two things.
