I had this problem a few months ago with a MacBook Pro (Late 2012) , I tried everything , hardware tests , erase the disk .
In the genius bar did not know what the problem was after several visits to the genius bar , I told them I could not continue going and that only erased and returned me .
Then to have taken her many times to repair , I had my data on an external hard drive, load the iTunes library from an external hard drive and never paused .
( To load the iTunes library from a different disk to the original , press " option key " to start iTunes, and you will leave the file chooser , iTunes Library.itl selected from the eternal hard drive).
So l told them that had occurred with the hard drive although their hardware tests did not detect the error , it was clear that the hard drive was what was causing it .
In your case to have a MacBook Pro Retina, the problem must be with the SSD , changing the hard drive in my case everything was solved , and they offered me apologize for not having realized before that there was error, since their hardware tests do not detect the error.
Greetings and I hope will be useful .
( Sorry my English is a bit bad).