Too many boot problems... PLS HELP

[crit]

Hey guys,
so 2 days ago I left my computer while it was running and I came back to a black screen saying
"Boot Manager missing. Press Ctrl + Alt + Delete to restart".

In an attempt to fix the problem restarted the PC and checked my boot order in the bios with no success . I tried fixing it by inserting the installation disc and choosing the "Repair Option" but it told me something along the lines of "Your copy of Windows is not compatible with this version of Windows...blah blah blah" Note: No i didn't pirate windows, I paid for it.

Then i reseated all the SATA cables and on the 3rd restart (booting from the disk) it magically loaded my old desktop (don't ask me how). Then everything was fine for a day until my computer froze, i restarted it and the black screen with "Boot manager missing etc" appeared again.
I went through all methods i listed above to fix it, again with no success at all.

So then i decided to do a clean install of windows on a spare 300GB HDD, so that I could then backup my SSD to my another 2TB HDD and then do a clean install of windows on my SSD. (it took a solid 13 hours to back everything up at a speed of 1MB/s, is that slow or what?)
Then attempting to reinstall windows it told me that my previous partitions on my ssd were in the wrong file system, which prevented me both from installing it on SSD and formatting the partition (so I thought maybe this was the problem all along), the only thing I could do was to erase the partition and create a new one. Fortunately this worked and it installed a clean version of windows on my SSD (boot times however are not SSD like at all).

Now after restarting the PC a few times to install drivers etc the issue came up AGAIN. "boot manager missing...". Again i check my boot option in the bios and magically a new option has appeared "Windows Boot Manager" and forcing the PC to boot off that took forever but it loaded the new install of windows i have just made.

I am really sorry for the essay but this is the first time something like this has happened to me (and I'm out of ideas on how to fix it myself).

1. Does anybody know what is actually wrong?
2. If everything is normal, why does it take years to boot from the SSD (Windows Boot Manager)
3. It created 3 (2 for windows 1 for normal use) partitions on my SSD instead of 2 like last time. Why??
4. For some reason my 2tb hard drive that has all my files on it is now set to read only, it doesn't let me change it to normal and I can't access most folders saying "You need admin priviledges. Click continue" which i do but the loading bar to give me those admin rights never completes. WHAT IS HAPPENING?!?!?!

To anyone that reads this essay and replies. Thanks in advance I'm out of ideas.

PC Specs:
i5 3570k
Gigabyte z77x-d3h
Barracuda 2TB HDD
Samsung 840 PRO 120GB SSD

 

[hang-the-9]

Outside of something like a virus messing with your system, try a BIOS updated on the motherboard, get a few new SATA cables to use, unplug all drives from the computer, install only the SSD you will be using, do a clean setup of Windows on that after deleting all partitions and creating a new one, don't plug in any other drives, run the driver setups for the motherboard, see how that runs. If it runs OK, install the second hard drive and check things then.

 

[SanoTooo]

Not much help from me, but I recently had some stumbling on reboot, Dell Dimension 4600 XP Pro, 2,8Ghz P4. Probably 9-10 years old.

When running machine is as good as it's ever been. Rebooting is a crapshoot. Blank screen with blinking hyphen in the upper left corner. I'm leaning toward some mobo component failing or getting some sort of (possibly broken) crap from a bad torrent. My s/w firewall isn't showing any particular increase in activity.

I had a difficult time rebooting to a Kaspersky 10 rescue disk. The first time the cd wasn't recognized, for no apparent reason. Just rebooting I often get the blank mentioned above. Then I play with the F12 and sometimes get the bios. and closing out it would boot to XP. Sometimes I'd get the boot selection screen. Which didn't always boot.

My 5 backups were marked damaged by one of the anti-malware or AV programs I ran.