File check on boot up?

I am a first time computer builder, my specs are as follows:
MSI|VIA K8T800 K8T NEO-FIS2R Retail
ATI RADEON 9800PRO 128M OEM
3000+ ATHLON 64 Retail
ZALMAN CNPS7000A-CU
DDRAM 512MB 32MX8 PC-3200C2 Corsairx2
1.44MB SONY MPF920 Beige
Western Digital 10,000 WD360GD 8MB Hard Drive OEM (its the 36gb Raptor)
FORTRON 530W Power supply (meet with atx12v specification)
CASE KINGWIN KT-424-BK
If you need more detail just tell me.
The system works fine, it is stable and runs games etc, well.  One thing though; everytime I cold boot the computer, that is, turn it on after it has been turned off for awhile, it pauses extra long at the screen that says "scanning devices please wait".  Eventually the pc boots into the windows loading screen, but from that screen instead of going to the windows welcome screen it goes to a blue screen that looks similar to the screen when windows xp is installing on a hard drive, this screen says:
Checking file system on C:
The type of the file system is nfts
etc....
After the computer is done with the check it reboots the pc and this time the pc boots normaly.
What gives?
Is this normal, if not what should I do to fix this?

1. if you are not using the promise controller, disable it in bios
2. looks like check disc is running for some reason. i don't know why though sorry. could be nopt shutting down correctly or something. is ACPI enabled?

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    MMAN started with pid=4, OS id=972
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