First, some keywords to help searchers:
QX9650, quad core, task manager, cpu-z, cpu-id, shows showing only 2 two cores.
I recently upgraded an Intel E8500 to a QX9650 and had the problem of Windows 7 only showing 2 of the 4 cores.
It took a few frustrating hours to find the solution, but I got there in the end without the need for a Windows re-install. I hope that this little post may help others to resolve the problem quicker than I.
1st: You must have Windows 7 Professional. Home Premium does not support more than 2 cores. Upgrade to Pro.
2nd: If Task manager and CPU-Z are only showing 2 cores, you'll be feeling pretty confused, right?
Go to Start-->Run, type MSCONFIG.
Under the BOOT tab, click 'Advanced Options'.
In the top left corner it says "Number of Processors" (you'll have been here already and it says '2').
Uncheck this and do a reboot.
This solved my hours of confusion. Now I have 4 cores in Task Manager, CPU-Z and all is well.
If all this fails, then get yourself set up for an OS reinstall; that should get you where you want to be.
I hope this helps folks a little as I had a hard time resolving this quickly.
I'm no expert but my sketchy understanding is that if you tell Windows you have no processors, it re-evaluates this at boot and discovers that you've changed from a 2 core to a 4 core.
Well, it worked for me and I hope it helps others out there.