MC's auto-import system doesn't run on a scheduled basis. It uses the Windows API to get notifications of changes to the file system. It doesn't often fail to pick up changes, but I have seen it happen once or twice.
As far as settings, if you want to make sure that files in your watched folders ALWAYS get picked up, make sure the "Ignore files previously removed" option is deselected for all of EACH of the folders you watch. That's probably not it since the manual auto-import grabbed it, but worth mentioning.