OS X Safari keeps forgetting cookies
Something you can attempt:


Enter Recovery mode (⌘ + R on startup)
Go to Utilities -> Terminal
Enter this command resetpassword and hit enter.
At the bottom of the window that appears, you will see "Reset Home Directory Permissions and ACLs". Click "Reset" and reboot.


This will hopefully resolve the permissions issue you're encountering, assuming it is rooted in a permissions issue- perhaps you manually migrated your user folder at some point?