Re: Chkdsk runs everytime computer is boot up
It is possible that the following registry key / value has been set to something other than its' normal default value
Check here
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControSet\Control\Session Manager
In the right pane the value of BootExecute should read autocheck autochk *
If it is something other than that double click it and edit it appropriately. See attachment.
Using the Windows Registry Editor can cause serious, system-wide problems that may require you to re-install Windows to correct them. It cannot be guaranteed that any problems resulting from the use of the Windows Registry Editor can be solved. If you choose to edit the Windows Registry please understand that you do so at your own risk so unless you feel fairly comfortable and confident you should probably not use the Editor. Changes made to the Windows Registry can take effect immediately and those that do not will take effect following the next reboot of your computer, and a current backup is not automatically made for you....So manually create a system restore point, backup the registry and export the key you are editing for safe keeping before doing so.
Yesterday was, Today is, but ahh Tomorrow...mystery, suspense and a promise of hope.

Operating System Windows 7 Ultimate 64 bit
Computer Type Home built
OS Service Pack Service Pack 1
Internet Explorer Version IE9
DirectX Version 11
CPU Type and Speed AMD Phenom II X6 1090T Black Edition Thuban 3.2GHz
CPU Cooling Stock Factory Cooler
CPU Idle Temp 32C
Motherboard Chipset GIGABYTE GA-870A-UD3 AM3 AMD 870
System BIOS Revision Award F5a (beta) 11/15/2010
System Memory Type G.SKILL Ripjaws Series 16GB (4 x 4GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10666)
System Memory Speed 1333 currently underclocked to 1066
System Memory Clocking 7, 7, 7, 20
Video Card Type and Speed Nvidia GeForce GTS 450 1Gig DDR5 DX11
Video Card Cooling stock
Video Card Temperature 32C idle
Power Supply Unit (PSU) Antec EarthWatts EA750 PSU
Computer Monitor Dual Dell ST2320L
Sound Card Integrated RealTek HDA
Speakers Klipsch
Headset/Microphone Altec Lansing
Hard Drive Two Seagate 500 gig SATAII's ST3500418AS ATA
Optical Drives Lite-On DVDRW x2
Keyboard and Mouse Logitech USB Optical
Modem-Router Type Arris MODEL: TM602G / Microsoft MN700
Network Adapter Realtek RTL8102E/RTL8103E Family PCI-E Fast Ethernet NIC
Printer HP InkJet 990cxi
Network Speed WD Passport 500gig USB 3.0 BackupDrive
USB Controller NEC Electronics USB 3.0 Root Hub
Gaming Console Xbox 360
Anti-virus Software Microsoft Security Essentials
Productivity Suite Office Pro Plus 2010
System Install Date 2011-01-25 21:59:23 on this drive
Computer Skill Level Certified Professional
Windows Experience Index 7.2
Favorite Game FarCry (original, 2 sucked)