Not sure about the X2's, if they do this or not, but it solved my disappearing core problem.
If you have Cool and Quiet enabled, it may shut down the cores not being used, and also lower the core speed of your CPU if it is not needed.
I noticed this with my PII 920, after a while if I was doing something simple and brought up the task manager, I noticed only 2 cores at times, and only 1 core at other times. Turn off Cool and Quiet and see what happens.
If that does not work, try simply deleting the processor from device manager, and let Windows reinstall it when it reboots.
Cool and Quiet also seems to never let your CPU run at full speed. With it enabled, my 3D mark 06 score was about 8500.
Turn it off, and I get over 15,000. Big, big, big difference.