I have never seen or read anything about his before, so here goes. I run KDE on X 7.2 on a gentoo system. I run the .8 version of the Baghira theme. I I have this one rogue green pixel that will sometimes show through some windows. It seems random. I will try and given an example.

I am browsing the net. While scrolling through a page dink! A pixel goes green. I think uh oh, one just died. But I can cover it with my mouse or with another window. So there goes that theory. Then if I uncover the pixel it still shows through the firefox window. Now if I scroll it will leave a little trail. If I move the window it will too. This trail is similar to a cursor trail. I will then minimize the window and bring it back and the pixel is gone, but will probably show back up later on. The desktop normally has 1 green pixel. Usually it doesn't come up in game. Has anyone ever seen this?

sounds like a bad address in your video memory. the trails are caused by cloning of the bad pixel (it is still read as something).
while the bad pixel remains in that spot in some page of memory, others are just a copy of it.
i never had to do this before but there should be some memory checking utilities for video cards...
try lowering the clocks or something and see if it goes away...
just a wild guess.