I'm having the exact same problem as "erbipjr".
Put together a computer with brand new components, and it works fine except if I powerdown the computer; when I cold boot the computer, WinXP starts with the:
Windows could not start because the following file is missing or corrupt: \Windows\System32\Config\System
If I wait about 10 minutes, and warm boot, WinXP starts fine. Sometimes if I don't wait the 10 minutes and warm boot, may WinXP will start but with permanent corruption (mirrored desktop, Explorer fails to start, etc).
Stuff I've tried/checked:
-WinXP SP2, SP3 & Vista SP1
-installing latest drivers
-flashing with latest BIOS
-swapping my SATA2 drive for an IDE drive
-AHCI enable/disabled
-Hitachi Drive Fitness Test: no errors
-memtest86: no errors
-disable ACPI & wake-on
-memory: dual channel, single channel, single module in different slots
-low level formatting drive & boot sector
-disabling write caching within XP & in hardware
-safe mode
-diagnostic startup via XP msconfig
-reconnect all cables
-swapping DVD-R drive with a CD-RW drive
-AMD Overdrive stability test: no errors (I have not overclocked ANY of the components yet)
-increasing memory voltage to 2.1V (OCZ recommendations)
-lowering memory to DDR2-667
-tested hard drive in another computer
-stock BIOS settings, misc BIOS changes, Optimized settings, reset CMOS, etc.
-disabling non-essential drivers
-swapping mice
-putting DVD-R drive as slave or master
-adding 15 second boot delay in BIOS for hard drive spin-up
-Event Viewer shows no problems
-all temperatures are below 40 degree celcius
-repartitioning drive
...and many other random attempts.
Note: I re-installed WinXP SP2 with almost every attempt I tried. (To the point where I'm ready to make an unattended install CD just for this computer.

)
I suspect something in the hardware: motherboard or power supply. Possibly RAM, though it passed MEMTEST86 and AMD Overdrive stability tests.
Any ideas on how I can narrow it down to what's causing the problem? Unfortunately I don't have access to many spare components, so any help in diagnosing the problem before buying replacement parts would be appreciated.
Thanks!