To anyone who can have similar problems:
I was having this problem with overclocking - On a fresh reboot all stability and stress tests would pass without any glitch. But overnight when I would run the tests again they would fail, rendering me and my overclocking attemps very frustrated. Something was happening after some hours, and I tended to think it was the hardware and the voltages were failing.
I started having these dreadful nightmares and these two huge bags appeared under my eyes, started walking around like I was a zombie with this voice inside my head banging all the time - " your overclock is very naughty, ahhhhahhh" ;D
Then, I found out that my paging file was the culprit, the damn thing on auto would change on its own and would force errors on stress testing programs because of the memory block size..
So I found my way around the correct paging file size for my memory size (16 Gb) and now the stability tests will run the same way either on fresh boot or after long hours of up time.