Windows 7 fails to start after shut down

I have Windows 7 Home Premium 64-bit on a 2-year old Lenovo SL510 laptop.

This is the current issue: Windows fails to start after the computer shuts down. It gets to the Windows logo load screen and then goes black and does not respond to anything.

This is the full story: At first, explorer.exe failed to load after I logged on. I could see a cursor and run programs through the task manager, but running explorer.exe yielded nothing. I ran a virus scan and it found a trojan (!) but afterwards the problem persisted. I backed up my data and reinstalled windows.

At this point my current problem started. I can restart the computer or put it to sleep or hibernate, but if I shut it down it won't come up. Startup fixing when booting from the installation disc does nothing, but system recovery works. I've reinstalled and recovered several times until I figured out that shutting it down is the issue. I ran a disk-check, it fixed some bad sectors but I don't know if that's relevant.

I would be glad to hear any suggestions on what to try next.

EDIT: The PC was hibernating for two days, and once I turned it on it displayed:

"The computer can't come out of hibernation

Status: 0xc000009a

A fatal error occurred processing the restoration data

File: \hiberfil.sys"