Windows 7 won't start after changing permissions (black screen)

After changing some permissions I cannot get into my computer and can't even boot into safe mode. I can only boot with Windows 7 Recovery CD. Startup repair won't fix anything but I can use command prompt (cmd) and get into regedit.

I have been able to change the following key value as advised here: https://ccm.net/computing/hardware/1535-computer-boots-to-black-screen/ But for some reasons the settings won't apply and I would still get black screen with moving cursor. Ctrl+Alt+Del won't work.

Mouse cursor is visible and movable. I have read that it is due to some file permissions. I have already took ownership and granted full control to Administrators and SYSTEM.

When I use Recovery CD there is system restore that won't work, Startup repair won't work either, I can only use command prompt that starts with X:\Sources>.

The command prompt is entitled Administrator: X:\windows\system32\cmd.exe
My OS is intalled on C: drive, however. The drive is active and partitions are OK. Should I somehow change that X:?

Any help would be much appreciated.