Please look at the image below. It shows me attempting to point to something in an always on top window. But I can't see what I am pointing at because the cursor shown by CursorFX is below the window.
I'm having the same problem, the cursor disappears behind certain windows, like the Yahoo widgets and Seesmic Desktop yet it does appear in front of browser windows and Trillian. I'm using the latest version of the program with Windows XP (though I don't have the problem with my laptop running Vista).
Any help would be appreciated.