Also, when I mouse over the "All Programs" part in the start menu (more programs in Skin Studio), it totally blacks out and looks like this:
Hmm that mouse over the text is green.... here anyway.. its black mouseover with green fonts instead of an image there
and i see the icons in more programs is to much to the left....
the tabs in ie is skinned only works in ie7+6? also the selection.. where it is black over your browser target that is supposed to be green.... with black text. The bookmark field(?) text i dont know if it is changeable.. its the toolbar background.. and ofc the explorer navigation buttons is not aligned but i dont think that is possible to correct, think i read about it in another thread?
Systemtray icons should not change size... neither quicklaunch... they stay the same witchever skin you use:)
And it looks like the taskbar buttons arent displayed correctly but cant be sure can u give me a full screenshot?
Im redoing all fonts to a green color... ill send you a copy later on see if it works better...
And check if you are running sRGB(the most commonly used) color profile on your monitor... and calibrate... 
And it might be lighter here for me because im on a LCD...