Oh, Never mind, I know what you're talking about. Its a limitation of flash
Let me guess, you scrolled down on the screen, and the mouse didn't keep up? Theres two solutions I can think of:
1/ When you're scrolling down the screen, keep your mouse within the navcomp [Yeah, sounds wierd, but its a wierd problem].
2/ Load up the SWF directly, and it should resize to be the browsers size [so no scrolling, which stuffs it up]. To load it up directly, click here: http://swcombine.com/navcomp/navcomp.swf
Everything will be a bit smaller on the screen, but no scrolling = no mousecoords problem
If theres still a problem, post here again please, with some more details where it stuffs up.