After four long days of hard struggling
trying to make my main hard disk to be able to boot a system again and researching a bit, I discovered that this HD had all the symptoms of a rootkit.
Apparently they like to live at the kernel level, they use to be injected while installing drivers, and they use to fuck up your MBR... exactly what I was doing and what happened. Plus, formating doesn't help. Exactly what happened to me. Installed like eight different systems with different grub options. Nothing worked even after a low level formating. Scanning and trying to discard damaged or faulty HD sectors reported nothing wrong in the entire disk. Everytime GRUB failed to boot. The systems were bootable from the GRUB in my second drive. The only solution I've found is going for GPT partition table. This has a smaller 64 MB efi_grub partition instead of the 446 or thereabouts for GRUB, or 512 MB in total including 64 MB for the partitions in a DOS partition table. This excluded the screwed up part from the equation altogether and finally the HD is bootable again. I was about to trash it and buying a new one... phew!
I cannot tell for sure if it's a rootkit there, but given my recent damned experience, be careful if you use smxi to instal Nvidia drivers. And better have rkhunter and/or chkrootkit on hand. I had no idea of this in advance and it gave no time to react. Chose to install the drivers and then all went south. No way to fix my system or booting it again. All destroyed and gone in seconds. Perhaps downloading only and running rkhunter before doing anything might be a wise option.
Well, I think I've had my first rootkit experience. I'm not a virgin anymore... but I don't recommend the experience to anyone. BTW, Fucking bastards! Why they do this?