Is your CPU an AMD? if so...
There are several options:
1)Windows XP Hotfix
2)AMD Patch
3)Set Affinity
4)Hide the core.
since you mentioned hiding the core I'll go with that one. This fix requires a Sys Config Utility tweak.
Run msconfig from the start menu, click the BOOT.ini tab and click the Advanced Options button. Check the box entitled /NUMPROC= and set it to 1
Click OK. Reboot and verify by r-clicking Taskbar and clicking Task Manager. Navigate to the Performance tab and under CPU Usage History you should see 1 CPU graph, not 2.
Personally I would try the AMD patch first:
To do this manually r-click My Computer select Properties. Click the Advanced tab, and select Startup and Recovery. Click the edit button and edit the boot.ini file. Add at the very end:
/usepmtimer
The final line should look something like this:
/Fastdectect /Noexecute=Optout /usepmtimer
This fix did not sync my cores, but did seem to stabalize it for gaming. Before I did this HL2:E1 was locking up every 2-10 minutes. After, not at all.
NOTE: Make sure that you create a system restore point before you start.
You can also download it from the AMD website. I did it manually as it was faster and easier.
Before you try any of these I would read up so you know what you are doing, not simply editing files. Have an idea of what is occuring logically.
Hope this helps