My mail rules don't stay on
Sounds like your Mail preferences are not saved.

Try this (it is not same as using Disk Utility to repair permissions)


  You can use the ACL tool on the Recovery HD to do this:
  
  
  Boot into the Recovery HD using ⌘R.
  Run resetpassword in Terminal (available from Utilities → Terminal).
  Select your account from the drop-down list.
  Click the Reset button for Reset Home Directory Permissions and ACLs.
  


Source: grgarside — https://apple.stackexchange.com/a/110346/

If you are not comfortable doing it above way, there is a application called OnyX that will do it for you (and much more).