1) Uncheck in MSConfig > Boot tab > Advanced Options > "Number of Processors" and exit MSConfig
2) d/l and install an applet called EasyBCD 1.7.2 (or later, Google: EasyBCD) which supports many features of Windows 7.
3) Go into Advanced Options in EasyBCD and select "Limit Widows to '0' CPUs (Leave 0 to reset)". Click "Apply Settings" and exit EasyBCD.
NOTE: This will force the OS to reset the count to default for the amount of Cores you now have. There is possibly a boot setting that can be added that I may not be aware of to do this same function but this little applet works and does the same thing. Don't muck around with any other setting in this utility if you don't know what you are doing it may leave your computer unbootable and a complete reinstall or long repair may need to be performed. Just make sure this one setting is set to "0"
4) Completely shutdown the OS (not reboot or restart or logout). Correctly Shutdown you computer so the it powers down.
5) upon restart into the OS the Task Manager > Performance tab should now show the correct amount of per core graphs if you have the "One Graph per CPU" option selected. Should be good to go.
I dug this up on the Microsoft forums.
Multiple things can cause this, changing processors and even installing new GPU cards.
Hope it puts you on the right path.