I've had this issue both with Elementary OS and Xubuntu which both run Ubuntu 14.04 LTS. Every time I would boot up either Elementary or Xubuntu I would be left with my primary monitor working and my secondary monitor would not be working.
Occasionally after tinkering with the display settings I would get it to appear only for it to disappear after I turn my secondary monitor on and off or do a reboot.
A bug report has already been posted for it on launchpad: https://bugs.launchpad.net/ubuntu/+bug/1313539