Ok done. Folding now with all my cores. Thanks to voyager.
If any one else has any issues folding on all cores.
Here is the link again
http://folding.stanford.edu/English/WinSMPGuide
1.Download the client
2.Rename it FAH6
3. Make a folder C:\FAH6
4.Copy the client in the folder
5.Run Command Prompt as an Administrator
6. Navigate to the FAH6 folder using cd .. and cd FAH6
7.Type in fah6.exe -configonly -smp
8.Configure it, using your CoFo Username and team id.
9.Once you have gone through all the settings.Exit the client.
10.Do step 5 and 6 and then type in fah.exe -smp