duplicate settings files causing database cron and civimail error

I backuped a CiviCRM Site running 4.6 with a settings file I have been copying with every installation since version 4.6

After restoring and migrating to a new server I did the same procedure again and copied the settings file in
http://www.mysite.org/wp-content/plugins/civicrm/

I run the upgrade script for 4.7 and everything seemed fine.

however running a cron job was almost impossible until I discovered that I have two settings files. The other one is located in
http://www.mysite.org/wp-content/uploads/civicrm/
regarding the cron job only the site key in http://www.mysite.org/wp-content/uploads/civicrm/
leads to execution

I tried to remove the old 4.4 settings file, but when I do that I lose all my scheduled and archived mailings. Nothing shows up in the "scheduled malings". I tried to understand what is the difference between the two files, and why I need two settings files.

I am attaching the two settings files. Can someone please help me.
It is still possible to run the cron jobs by hand, but It seems my system is incomplete.