I recently built a computer;
AMD Athlon 64 X2 6000+ Windsor 3.0GHz
ASUS CROSSHAIR AM2 NVIDIA nForce 590 SLI MCP ATX AMD Motherboard
BFG Tech BFGE86256GTSOCE GeForce 8600GTS 256MB 128-bit GDDR3 PCI Express x16
CORSAIR XMS2 2GB (2 x 1GB) 240-Pin DDR2 SDRAM DDR2 800 (PC2 6400) Dual Channel Kit
Western Digital Caviar RE WD3200YS 320GB 7200 RPM SATA 3.0Gb/s Hard Drive / OS installed here
Western Digital Caviar RE2 WD5000ABYS 500GB 7200 RPM SATA 3.0Gb/s Hard Drive
Maxtor 500gb 7200rpm IDE Hard Drive
COOLMAX CUG-700B ATX 12V( V.2.2) 700W Power Supply.

The problems started when I installed Win XP pro. The system seems to run glitchy it will pause for no reason at random times for 30sec or more and then run fine again. When I open a program it can take from 30sec to 1min to open at times. When ever I try to save a file to the desktop it takes a long time to show the desktop in the save window. This only happens when trying to save to the desktop. When I try and open a file on my network it take a long time to open. There is an overall feeling when using the system that something is not running right. I have had issues with transfering files between HD's but that seems to be fixed now. I have run Chkdisc and there were no error reported. Please help in identifying the cause of and how to fix these problems.

Here is the Hijacktihis file

Running processes:
C:\WINDOWS\System32\smss.exe
C:\WINDOWS\system32\winlogon.exe
C:\WINDOWS\system32\services.exe
C:\WINDOWS\system32\lsass.exe
C:\WINDOWS\system32\svchost.exe
C:\WINDOWS\System32\svchost.exe
C:\WINDOWS\system32\spoolsv.exe
C:\WINDOWS\Explorer.EXE
C:\Program Files\Analog Devices\Core\smax4pnp.exe
C:\Program Files\Analog Devices\SoundMAX\Smax4.exe
C:\Program Files\ASUS\AI Booster\OverClk.exe
C:\Program Files\Multimedia Card Reader\shwicon2k.exe
C:\WINDOWS\system32\RUNDLL32.EXE
C:\Program Files\Softwin\BitDefender10\bdmcon.exe
C:\Program Files\Softwin\BitDefender10\bdagent.exe
C:\Program Files\HP\HP Software Update\HPWuSchd.exe
C:\Program Files\HP\hpcoretech\hpcmpmgr.exe
C:\WINDOWS\system32\rundll32.exe
C:\Program Files\iTunes\iTunesHelper.exe
C:\Program Files\Common Files\Apple\Mobile Device Support\bin\AppleMobileDeviceService.exe
C:\WINDOWS\system32\ctfmon.exe
C:\Program Files\Common Files\LightScribe\LSSrvc.exe
C:\Program Files\Google\GoogleToolbarNotifier\GoogleToolbarNotifier.exe
C:\Program Files\Common Files\DataViz\DvzIncMsgr.exe
C:\Program Files\GetRight\getright.exe
C:\Program Files\Palm\Hotsync.exe
C:\Program Files\HP\Digital Imaging\bin\hpqtra08.exe
C:\Program Files\Common Files\Microsoft Shared\VS7Debug\mdm.exe
C:\Program Files\NVIDIA Corporation\NetworkAccessManager\bin\nSvcIp.exe
C:\WINDOWS\system32\svchost.exe
C:\Program Files\Common Files\Softwin\BitDefender Communicator\xcommsvr.exe
C:\Program Files\Common Files\Softwin\BitDefender Update Service\livesrv.exe
C:\Program Files\NVIDIA Corporation\NetworkAccessManager\bin\nSvcAppFlt.exe
C:\Program Files\Cloudbrain\FixTunes\FixTunes.exe
C:\WINDOWS\system32\HPZipm12.exe
C:\Program Files\iPod\bin\iPodService.exe
C:\Program Files\Mozilla Firefox\firefox.exe
C:\Program Files\Common Files\Softwin\BitDefender Scan Server\bdss.exe
C:\Program Files\Softwin\BitDefender10\vsserv.exe
C:\Program Files\Trend Micro\HijackThis\HijackThis.exe

R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Page_URL = http://go.microsoft.com/fwlink/?LinkId=69157
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Search_URL = http://go.microsoft.com/fwlink/?LinkId=54896
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Search Page = http://go.microsoft.com/fwlink/?LinkId=54896
R0 - HKLM\Software\Microsoft\Internet Explorer\Main,Start Page = http://go.microsoft.com/fwlink/?LinkId=69157
O2 - BHO: AcroIEHlprObj Class - {06849E9F-C8D7-4D59-B87D-784B7D6BE0B3} - C:\Program Files\Adobe\Acrobat 7.0\ActiveX\AcroIEHelper.dll
O2 - BHO: GetRight IE Download Helper - {31FF080D-12A3-439A-A2EF-4BA95A3148E8} - C:\Program Files\GetRight\xx2gr.dll
O2 - BHO: Google Toolbar Helper - {AA58ED58-01DD-4d91-8333-CF10577473F7} - c:\program files\google\googletoolbar1.dll
O2 - BHO: Google Toolbar Notifier BHO - {AF69DE43-7D58-4638-B6FA-CE66B5AD205D} - C:\Program Files\Google\GoogleToolbarNotifier\2.0.301.7164\swg.dll
O3 - Toolbar: &Google - {2318C2B1-4965-11d4-9B18-009027A5CD4F} - c:\program files\google\googletoolbar1.dll
O4 - HKLM\..\Run: [SoundMAXPnP] C:\Program Files\Analog Devices\Core\smax4pnp.exe
O4 - HKLM\..\Run: [SoundMAX] "C:\Program Files\Analog Devices\SoundMAX\Smax4.exe" /tray
O4 - HKLM\..\Run: [NvCplDaemon] RUNDLL32.EXE C:\WINDOWS\system32\NvCpl.dll,NvStartup
O4 - HKLM\..\Run: [nwiz] nwiz.exe /install
O4 - HKLM\..\Run: [AsusStartupHelp] C:\Program Files\ASUS\AASP\1.00.16\AsRunHelp.exe
O4 - HKLM\..\Run: [Launch Ai Booster] "C:\Program Files\ASUS\AI Booster\OverClk.exe"
O4 - HKLM\..\Run: [Sunkist2k] C:\Program Files\Multimedia Card Reader\shwicon2k.exe
O4 - HKLM\..\Run: [NvMediaCenter] RUNDLL32.EXE C:\WINDOWS\system32\NvMcTray.dll,NvTaskbarInit
O4 - HKLM\..\Run: [BDMCon] "C:\Program Files\Softwin\BitDefender10\bdmcon.exe" /reg
O4 - HKLM\..\Run: [BDAgent] "C:\Program Files\Softwin\BitDefender10\bdagent.exe"
O4 - HKLM\..\Run: [HP Software Update] "C:\Program Files\HP\HP Software Update\HPWuSchd.exe"
O4 - HKLM\..\Run: [HP Component Manager] "C:\Program Files\HP\hpcoretech\hpcmpmgr.exe"
O4 - HKLM\..\Run: [DXDllRegExe] dxdllreg.exe
O4 - HKLM\..\Run: [QuickTime Task] "C:\Program Files\QuickTime\QTTask.exe" -atboottime
O4 - HKLM\..\Run: [iTunesHelper] "C:\Program Files\iTunes\iTunesHelper.exe"
O4 - HKCU\..\Run: [ctfmon.exe] C:\WINDOWS\system32\ctfmon.exe
O4 - HKCU\..\Run: [swg] C:\Program Files\Google\GoogleToolbarNotifier\GoogleToolbarNotifier.exe
O4 - Startup: Palm Registration.lnk = C:\Program Files\Palm\register.exe
O4 - Startup: palmOne Registration.lnk = C:\Program Files\palmOne\register.exe
O4 - Global Startup: DataViz Inc Messenger.lnk = C:\Program Files\Common Files\DataViz\DvzIncMsgr.exe
O4 - Global Startup: GetRight - Tray Icon.lnk = C:\Program Files\GetRight\getright.exe
O4 - Global Startup: HOTSYNCSHORTCUTNAME.lnk = C:\Program Files\Palm\Hotsync.exe
O4 - Global Startup: HP Digital Imaging Monitor.lnk = C:\Program Files\HP\Digital Imaging\bin\hpqtra08.exe
O8 - Extra context menu item: Download with GetRight - C:\Program Files\GetRight\GRdownload.htm
O8 - Extra context menu item: E&xport to Microsoft Excel - res://C:\PROGRA~1\MICROS~2\Office10\EXCEL.EXE/3000
O8 - Extra context menu item: Open with GetRight Browser - C:\Program Files\GetRight\GRbrowse.htm
O9 - Extra button: (no name) - {e2e2dd38-d088-4134-82b7-f2ba38496583} - C:\WINDOWS\Network Diagnostic\xpnetdiag.exe
O9 - Extra 'Tools' menuitem: @xpsp3res.dll,-20001 - {e2e2dd38-d088-4134-82b7-f2ba38496583} - C:\WINDOWS\Network Diagnostic\xpnetdiag.exe
O9 - Extra button: Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O9 - Extra 'Tools' menuitem: Windows Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O16 - DPF: {0E5F0222-96B9-11D3-8997-00104BD12D94} (PCPitstop Utility) - http://www.pcpitstop.com/pcpitstop/PCPitStop.CAB
O16 - DPF: {6E32070A-766D-4EE6-879C-DC1FA91D2FC3} (MUWebControl Class) - http://www.update.microsoft.com/micr...?1185136624718
O23 - Service: Adobe LM Service - Adobe Systems - C:\Program Files\Common Files\Adobe Systems Shared\Service\Adobelmsvc.exe
O23 - Service: Apple Mobile Device - Apple, Inc. - C:\Program Files\Common Files\Apple\Mobile Device Support\bin\AppleMobileDeviceService.exe
O23 - Service: Autodesk Licensing Service - Autodesk - C:\Program Files\Common Files\Autodesk Shared\Service\AdskScSrv.exe
O23 - Service: BitDefender Scan Server (bdss) - Unknown owner - C:\Program Files\Common Files\Softwin\BitDefender Scan Server\bdss.exe
O23 - Service: ForceWare Intelligent Application Manager (IAM) - Unknown owner - C:\Program Files\NVIDIA Corporation\NetworkAccessManager\bin\nSvcAppFlt.exe
O23 - Service: Google Updater Service (gusvc) - Google - C:\Program Files\Google\Common\Google Updater\GoogleUpdaterService.exe
O23 - Service: InstallDriver Table Manager (IDriverT) - Macrovision Corporation - C:\Program Files\Common Files\InstallShield\Driver\11\Intel 32\IDriverT.exe
O23 - Service: iPod Service - Apple Inc. - C:\Program Files\iPod\bin\iPodService.exe
O23 - Service: LightScribeService Direct Disc Labeling Service (LightScribeService) - Hewlett-Packard Company - C:\Program Files\Common Files\LightScribe\LSSrvc.exe
O23 - Service: BitDefender Desktop Update Service (LIVESRV) - SOFTWIN S.R.L. - C:\Program Files\Common Files\Softwin\BitDefender Update Service\livesrv.exe
O23 - Service: NMIndexingService - Nero AG - C:\Program Files\Common Files\Ahead\Lib\NMIndexingService.exe
O23 - Service: ForceWare IP service (nSvcIp) - NVIDIA Corporation - C:\Program Files\NVIDIA Corporation\NetworkAccessManager\bin\nSvcIp.exe
O23 - Service: NVIDIA Display Driver Service (NVSvc) - NVIDIA Corporation - C:\WINDOWS\system32\nvsvc32.exe
O23 - Service: Pml Driver HPZ12 - HP - C:\WINDOWS\system32\HPZipm12.exe
O23 - Service: BitDefender Virus Shield (VSSERV) - SOFTWIN S.R.L. - C:\Program Files\Softwin\BitDefender10\vsserv.exe
O23 - Service: BitDefender Communicator (XCOMM) - SOFTWIN S.R.L - C:\Program Files\Common Files\Softwin\BitDefender Communicator\xcommsvr.exe

Yes I reformatted the HD's before installing. I changed the SATA cables positions on the motherboard and it seemed to fix the problem. I think the two HD's tried to reference the same memory and it crashed the system.

did you format all the hds? if you did did you change the jumpers to slave and not master? or it might just be you hd are not workable whit each others well thats my saying im just a noob but thats what happen to mine and wipeing them out and changing the jumper to slave and keep the one that you install you os on as you master im a noob but thats what i have to say