It probably sounds silly, but accurate timekeeping on a PC is incredibly difficult from a software and hardware point of view (speaking from experience as someone who has programmed everything from assembly code up to interpreted languages on x86).
There are many different clocks - all running at different speeds - inside a typical PC: the BIOS clock everyone is familiar with, internal CPU clocks, sound card clock, network card clock, power management controller clock, and so on. They naturally/physically run at different speeds, but the operating system also has to switch between them due to hardware constraints.
I'd probably try to start by isolating what the likely problem is: disable time updating over the internet, unplug as many external devices as you can (including ethernet/wifi), and boot the computer in safe mode. Don't load any applications and just leave it running.
If the clock still runs wild, then the culprit may be a driver/kernel issue, or something related to core hardware (e.g. ACPI - power management controller).
If the clock happens to be "fixed", then you can figure out what device/application is causing the problem by a process of addition / elimination.
If it's an internal Windows driver issue, here are some pointers to start looking (ACPI issue, MaxAllowedPhaseOffset setting, etc):
http://social.technet.microsoft.com/...-fbba6fc9324e/
Also - much like how even with autoguiding you still want a mount that has very smooth PE that can be guided out (think of remote time synchronisation as being like autoguiding), you'll probably want to fix the underlying problem otherwise you may introduce new issues. Most timing loops in software is written with the expectation that time runs forward and smoothly - excessively frequent clock corrections will likely cause problems.
Good luck!
