Thanks for testing.
Windows' timers are somehow not running as they should.. But you should see the same thing in other stuff, a lot of games and other apps use the same timing functions as the mod does. It's nearly impossible that this problem happens just with superpi, it's not like it uses some kind of magic timer, uses regular timing functions that are widely used by other apps I'd be suprised if the windows clock runs as it should, because I think it should run a few % too slow.
I'll slap together a test app with different timing methods to see if there's any that actually runs at correct speed. Will post it here when I'm done