I had the same problem, found a fix today, works so far <knock on wood>.
The problem is as follows:
The AMD CPU drivers for dual core change the behavior of the Windows API calls QueryPerformanceCounter and QueryPerformanceFrequency used for high-resolution timing so that they return the CPU cycle counter rather than the 3.54MHz chipset clock counter. This causes problems because a) CPU clock speed varies with Cool n' Quiet and b) The 2 cores cycle counters may not stay 100% in sync, which can cause negative time measurements and overflow errors when a process switches between cores.
To fix it, add a "/usepmtimer" switch to the end of the line specifying your MCE install in boot.ini to make it go back to using the 3.54MHz clock.
For example, if your boot.ini contains
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Windows XP Media Center Edition" /fastdetect /NoExecute=OptOut
change it to
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Windows XP Media Center Edition" /fastdetect /NoExecute=OptOut /usepmtimer
Reboot and the problems should go away.
BTW, the "hosed" recorded shows will play smoothly in Windows Media Player 10, however it will think the show is longer than it is, and scrolling the time bar to skip commercials won't work exactly how you would expect.