I discovered exactly the same thing when using the 3D vision system with an old fashioned CRT. Heavy ghosting at the top and nearly no ghosting at the bottom.
This must be a synchronisation issue. Since the emitter is no longer synchronized by a signal at the video output (which would of course perfectly be in sync) but through an USB port, the sync is purely "virtual". Unfortunatelly there seems to be no sync delay adjustment possible in the currrent 3D vision driver, even with registry hacks.
So all we can do at the moment is to hope that nvidia will include a sync delay adjustment in an upcoming driver release.
To get nvidias attention, you may post this problem in their 3D forum too:http://forums.nvidia.com/index.php?showforum=40