The latest version of WHM (11.25 I think) is pretty damn buggy, so if you are using WHM check your version and if you are on it use a service like pingdom to track the uptime.

What I woke up to was bad, hours of downtime just going up and down like a see-saw. Pages were either being sent to cPanel’s 404 pages or Installed successfully pages. I’m pretty sure there was a DNS issue somewhere.