I suspect your problem is a bad sector(s) on the hard drive.
In rare circumstances the normal mapping off process doesn't work, like it can't read the destroyed data, or your one of those people who are moving their laptop while it's in operation, which causes the heads to strike the platters and ruining data your machine requires to operate.
What your going to have to do is remove all your personal data off the drive.
Then command r boot the machine into Recovery HD, use Disk Utility to Erase (middle selection, important) the Macintosh HD partition, it will take some time to complete.
When finished quit and reinstall OS X from Apple's servers.
Your problem should be resolved, but if it returns, your likely going to need a new hard drive as it's failing.