Grey Screen with Flashing Folder with Question Mark

Question

Hi,
I need some help with an issue I'm having on my Mid-2012 Macbook Pro (13"; OSX 10.9.2; 8GB RAM).  I've had issues with this Macbook for the past year.  I've worked with Apple Support and had it into the Mac Store prior to the warranty expiring (Dec 2013).  I have the exact same model with all of the same specs that my employer purchased at the same time for work as my work computer, and I haven't had any issues with that one.
Previously, the system would slow down excessively and eventually start hanging. Occasionally the screen would start flashing.  Apple phone support had me wipe the hard drive and re-install the OS and all of my file, apps, and setting from my Time Machine backup.  That worked for about four months, and then it started again. Since it was getting close to the warranty expiration, I took it to an Apple Store. They ran a bunch of diagnostics, said the hardware was all fine but the OS needed to be re-installed.  They did that in early Dec, and everything was cool again until about three days ago.  Three days ago, it started slowing down and freezing again (even when doing non-memory intensive tasks such as broswing the web with only a couple of tabs open and no other applications open).  Last night, it froze hard and wouldn't shut down, so I had to cold boot it.  When I tried to power it back on, it came to the grey screen with the flashing folder with the question mark (which I know means it can't find the boot sector).  I waited until this morning, and it stil wouldn't boot. I then rebooted into Startup Manager, and the HDD was there. I selected the HDD, and it booted fine and ran fine for a couple of hours (I was able to do a Time Machine backup).  Then it froze up solid again. I waited for an hour or so before cold booting (don't like doing that), and when I tried rebooting, I got the flashing folder with the question mark. I tried booting into the Startup Manager again, but this time, my HDD wasn't listed. I then booted into the OSX Recovery utility (CMD R on boot), went into the Disk Utility hoping to do a disk repair, but my HDD wasn't listed. I have an external SATA to USB adapter, so I pulled the HDD, hooked it to a USB port on my other (identical except it doesn't have problems) Macbook Pro.  Once my other Macbook booted, the HDD from the bad Macbook Pro showed up fine.  I ran a verify and repair disk on the HDD from the bad Macbook, and it didn't show any issues.
So I figured I'd be really brave. I took the HDD from the bad Macbook Pro and put it in my work (good) Macbook Pro (I took the HDD out of my working work Macbook Pro).  It booted fine.  I then did the verify and repair disk (again no errors) and verify and repair permissions (it found a few, but no more than it has in the past). I ran it that way for about an hour with no issues. That led me to believe that the HDD for my personal Macbook was fine, and it must be an issue with the SATA cable or the mainboard. 
Here's where it gets odd.  I put the HDD from my work Macbook Pro into the bad Macbook Pro thinking it wouldn't even recognize it.  It did recognize it, and it booted fine.  I ran it like that for about 30 minutes.  It did have a couple of short freeze ups, but it didn't lock up solid. I didn't want to push my luck and possibly damage the HDD for my work Macbook, so I shut down the bad Macbook Pro ended the experiment at that point.
I put the original HDD back in the Macbooks where they originally came from. I then ran the Apple Hardware Test (press and hold D on startup) on the bad Macbook Pro; I did the extended testing option. It ran for about an hour, but it didn't find any issues with the bad Macbook Pro. 
I put the HDD from the bad Macbook back in my working Macbook and wiped the disk and reinstalled OSX from a Time Machine Backup from last week (before the problems occured).  Put it back in the bad Macbook and still no luck. Finally I tried resetting the PRAM because I saw that as one of the options on this discussion board. 
I've searched and read everything I can find related to this, but I can't find anything that works, and I'm at my wits end.  Can anyone point me in a direction of what might be wrong and what else to try?
Thanks!
Mike

Answer 1

You performed thorough and methodical troubleshooting, and this appears to be the most important result:
I put the HDD from my work Macbook Pro into the bad Macbook Pro thinking it wouldn't even recognize it.  It did recognize it, and it booted fine.  I ran it like that for about 30 minutes.  It did have a couple of short freeze ups, but it didn't lock up solid.
Given compatible hardware, you ought to be able to swap hard disk drives in exactly that manner, so it shouldn't surprise you that it worked. However, installing the "known good" HDD in the problem machine should not have resulted in any freeze-ups at all.
You can conclude the hard disks (both of them) are serviceable and whatever fault exists probably lies elsewhere. Often the SATA cable is damaged or not seated properly, and is likely to fail more than anything on the logic board. Inspect the logic board's SATA connections and make sure there are no contaminants or damage. The two drives and two logic boards are going to have slightly different component tolerances, so perhaps the defective one is simply exceeding some limit.
Apple Hardware Test is very cursory and essentially tests for the presence of operable hardware. It is far from an exhaustive test, and only a report of a failure can be relied upon for accuracy. For a more thorough test you would need to have Apple evaluate it using the time-consuming Apple Service Diagnostics. Even then, they may come up without a clue, and eventually someone will suggest a logic board replacement which can be expensive.
It is an unusual problem, and I don't know how much time Apple would invest in diagnosing it before they conclude you really ought to buy a new Mac instead. They might surprise you though in that a "depot repair", if yours is eligible, is a very cost effective option so consider it.
Given your ability you might also consider purchasing a replacement logic board from PowerbookMedic, or even sending it to them for a flat rate repair.