There was a relatively recent change to the default behavior. Many people on this list didn't like the fact that new entries got added to all of the publications. That seemed to be the overwhelming sentiment. FLEx was changed so that new entries only get added to the Main publication by default, and have to be added to any other publications manually.
At the moment, there isn't a way to configure what the default would be for new entries.
It is possible to sort entries by "Date Created", and then use Bulk Edit to assign Publications to entries created after a certain date.
-Beth