Thanks to a helpful developer at the ZSNES forum, I’ve found the solution to the VIA C7 platform speed/timing problems with certain programs.
Edit C:\BOOT.INI and add the /usepmtimer switch to the boot command line for Windows XP. This uses a timer that is stable even when in power management modes, which means that the throttling of the C7 CPU and accompanying chipset do not affect its timing characteristics. Some applications like ZSNES rely on a very precise and stable timing mechanism (in the case of ZSNES, speed regulation depends on QueryPerformanceCounter) and the normal timer on this platform is unstable in certain power management states. Also, I used WCPUID’s real-time clock display to figure out that the System control panel (sysdm.cpl) reports the frequency wrong on the C7 and that it is in fact running at 1200 MHz when under a full load, despite Windows’ insistence that somehow my CPU is going as low as 198 MHz when the lowest ACPI P-state is 400 MHz.
Now I can finally finish playing Final Fantasy V. 
