Also make sure not to use the TSC time source when using this program as this time source is included in the CPU and run at wrong speed after changing FSB.
You can accomplish this by adding a boot parameter from your boot manager "clocksource=hpet" or from command line with:
"echo hpet > /sys/devices/system/clocksource/clocksource0/current_clocksource"
If hpet is not available use acpi_pm.
Check /sys/devices/system/clocksource/clocksource0/available_clocksource for available clocksources.