Open the Task Manager (Ctrl + SHIFT + Esc) and select the “Performance” tab. Do you see all 6 cores (12 if you have hyper-threathing enabled) being utilized? If not, then there’s a BIOS setting or one in Windows that you need to change in order to enable all of your cores.
Each motherboard is different, so I can’t tell you exactly how to get there, but the windows setting in Windows 7 can be reached by typing “msconfig” (without quotes) in the search bar and pressing Enter. Select the “Boot” Tab and click where it says “Advanced options…”. You will see the option to choose the number of processors on the top left corner. Put a check mark on it and select the corresponding number. Close and restart the system. This shouldn’t be necessary, since Windows Vista/7 defaults to enabling all processors, but it could hopefully help you troubleshoot the issue.