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Problems with new computer

I bought and put together a new computer however I'm having problems. When looking at the task manager the processor use would jump from 0 to around 50% randomly like every few seconds when idleing. The "System" process seems to be the culprit, not the "System Idle Process". The harddrive makes a loud high pitched seeking sound that starts and stops but never seems to end, even after the computer has been idleing for a while. I get an very low sysmark04 score because of the graphics, the cpu scores seem to be ok. I get a very low 3dmark03 score (~6800). I've replaced the graphics card because I thought it was the problem but that was not the case. There are only a few things running in the task bar, Norton Antivirus and the usb wireless network card software.
A game that runs fine on a GeForce Ti graphics card lags with the 6600GT.
I've built computers for many years but I can't figure this problem out.

Here are the specs of my pc:

AMD Athlon64 3400+ Retail
Asus K8N-E Deluxe mobo
Corsair XMS 512 x 2 PC3200
WD 200GB 7200RPM SATA HDD
Jaton GeForce 6600GT AGP 8x
Creative SoundBlaster Audigy 2
Ultra X-Connect 500watt psu
Windows XP Home with SP2

 
Hi, how are you. I have some questions about your OS and other things about your Windows environment. Is this Windows XP? If so was it a fresh install? I'll be logged on from work today so I can check back pretty soon. Hopefully more people will come into the thread and we can get the problem figured out.
 
Have you installed the motherboard drivers? If it's running on Microsoft's generic AGP bridge driver, video performance will aweful.

 
Ok. I will assume that you are using the most up-to-date drivers and also updated your mobo BIOS.

- is your AGP set to 8x? some might be set to 4x by default
- have you scanned for adware/malware/viruses with the newest defs?
- the HD noise concerns me
- try running your benchmarks without any non-essential USB devices plugged in

i'm thinking the problem is something simple that you may have overlooked.
 
Have you tried defragging your harddisk? Harddisk noise is either seek trashing or a sign that your HD is about to die.

Not sure why System keeps going to 50% or so. Try shutting down all taskbar applications, and see if it still stays the same.

Creston

Edit : Btw, download the Microsoft AntiSpyware Beta, and let it run a deep scan. You may have spyware. Also get an antivirus program and check for virusses. (AVGFree works fine and is, as it says, free, or you can go to symantec.com and run a virusscan on their website, same for the guys who make PC-Cillin, their name escapes me at the moment).
 
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