My mail rules don't stay on I've setup one very simple rule that applies to messages from one sender... the rule works just like it should (most of the time).

Randomly, after I've restarted Mail the rule will be unchecked, so all of the new emails that were supposed to have been moved aren't. So I dutifully go i and check it back on when this happens, and drag the emails where they belong. this started when I up graded to Mavericks (a week or two after it was released). It has become very irritating by now, and I wanted to know if anybody else has had this problem and found a solution, or if somebody has a suggestion on what I could do to keep that rule checked off!
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).