Unable to startup MacBook, flashing question mark displayed

Today I opened up my MacBook to awaken it, to find the login screen had frozen- so I did a force-shut-down.

Upon start up; the familiar Apple drone was heard, no Apple logo was shown, and a flashing question mark was shown on screen.

I understand these symptoms are of a missing/corrupt OS.

I removed the affected startup drive from my MacBook, and connected it to a completely different computer (a Mac Mini) via USB.

I am able to successfully boot the Mac Mini using the affected drive, and everything works perfectly.

Why is it that my MacBook suddenly says my drive is corrupted/doesn't recognise the OS, yet another computer does?

[Background info]

• My computer is a late 2011 MacBook Pro running the latest version of OS X (at the time of writing).
• The original drive contained within the MacBook has been replaced by a SanDisk Ultra Plus SSD (256GB).
• This issue has occured twice before, the second time it occured I had the SSD replaced, so this rules out a hardware issue with the SSD... I hope.
• The SSD isn't running the latest firmware available to it, although I believe this shouldn't be a significant contributing factor.
• If I start up the computer and try to choose the startup disk, the only option available is Internet Recovery.
• The solution I have used the previous two times this issues has occured is to; clone the entire SSD using Carbon Copy Cloner (CCC), wipe and reformat the SSD, and then copy all the data back. Each time I've done this, one random particular file has failed to copy because it was corrupt. Last time it was a Matlab program file, and another time it was the app PopClip (downloaded from the Mac App Store). And then the computer works fine.
• Finally, my computer doesn't seem to recognise either of my two Time Machine backup drives, but that's another issue.

Message was edited by: moonfruit (spelling error)