Stop: 0xc0000218 {Registry File Failure}

Stop: 0xc0000218 {Registry File Failure} The registry cannot load the hive (file): SystemRootSystem32ConfigSoftware or its log or alternate. It is corrupt, absent, or not writable.

What could be wrong with my Windows 2000 or pc?

I get this and sometimes this error:

windows could not start because the following file i mising or corrupt:
windowssytem32configsystem

you can attempt to repair this file by starting windows setup using the orginal setup CD-rom.
Select "r" a the first sreen to start repair

I know how to fix them. I have fixed it several times. Through recovery console copying registry files from repair folders etc. But the main question:
WHY these errors apear? And only after i shutdown my pc. System is ACPI compatible. Errors apppear also when i shutdown pc with button and also when i simply start-shutdown. Maybe system makes shutdown too fast? Cause it shows : Windows is shutting down, 2-3 seconds and power off. Is it normal?
Plllllease help me to fix this problem. I didn't have these problems with windows XP, only with win2k. I checked memory, harddrive is 250 GB new WD (i had also one another hdd), i checked motherboard and all other hardware.
Maybe some problems with acpi?