Can not shut down late 2011 MacBook Pro and turn it back on again without the hard drive disappearing?

Ok, I have searched for months for an answer to this question to no avail, probably because no one has experienced it before. I am hoping however that you guys can help me figure this one out cause it is driving me nuts! Also, I am not entirely sure what section of the support I should put this under so if I stick it in the wrong place, I apologize.
Right now my problem is very simple. When I turn off my laptop, and then try to turn it back on, my internal hard drive disappears... and I get the blinking folder with a question mark on it. I have figured out something interesting however. I have an install disk with Ubuntu Linux on it. If I boot into that first, then RESTART the laptop, not shut down and turn back on, it reads the internal hard drive just fine and I can boot as if there is nothing wrong.
Second part to the problem... If I allow the laptop in either OSX or Windows to go to sleep (aka shut off the hard drive but the computer remains on), when I attempt to wake it up, I am greeted with the usual log in screen of whichever OS I am in, but is frozen and after a few seconds goes black and restarts the computer to find that... Surprise! The hard drive is gone
I have tried every trick in the book that I can think of, but can not seem to come up with a solution to the problem... I know when the problem happened and if anyone thinks that that will help them figure this out I will type everything I did up till, including the crash that caused this, and my attempted fixes, but I have class right now so only if you guys want it I will type all that out.
What I am currently running is:
2011 MacBook Pro 13in screen
4Gb of Ram
1TB internal Hard Drive
OSX 10.11.whatever the newest update is... just updated the other day again.
Windows 8.1 on BootCamp 5 (yea I know its not supposed to work but it does) again, fully updated
Ubuntu 13.10 (I think? Doesn't really matter, its just an install disk I use to boot the computer)
If there is anything else that you guys need me to provide, I can, just simply ask. I can provide as much info as is necessary.

Sorry it took me so long to write back, But unfortunately this didn't help my issue.
My uncle and I did a lot of tests on this computer and have narrowed down the location of the problem a little bit.
We tried to first reset the SMC and the NVRAM as suggested, but the only thing that did was make the fans run on full tilt for the first session after restarting it for some reason. After that we tried re installing OSX over the OSX that was already on the system (not removing any of the files). This also didn't do anything but make refit stop working. Then we moved onto the next task at hand by removing the hard drive entirely and booting it as an external drive from one of the USB ports... as long as you booted it with the options key held down, it worked perfectly fine. Then we put an alternative hard drive into the computer and installed OSX on that. This time there was no trouble booting anything up. Everything seemed to work flawlessly. So we made a backup of my original drive (OSX, Windows, and all) onto an external hard drive and tested booting to it via USB. That again worked perfectly fine and booted right up with no problems. So after that we formatted the original hard drive and reinstated OSX. We then proceeded to transfer all the old files from the backup onto this new installation and LOW AND BEHOLD..... we were back to square one with it refusing to recognize the hard drive again.
So this basically told us that there appears to be something either wrong with the hard drive, or something got really screwed up in the software along the lines and by me copying all my old files back over, I just ended up bringing the screwed up file back over with it! (despite not copying over any settings of any kind) So I am still extremely confused as to what is going wrong... did some boot sector possibly get screwed up may be?

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