FocusAlpha is a small utility program that will trigger Alpha Transparancy for all the windows on your desktop. When u select a window (set it on focus) it removes the transparency for that window and sets all the others transparent. The program allows you to control the level of transparency and you can also specify certain program names that you don't want to be transparent in the exclusion list.
If any program doesn't display correctly when transparent then add it's name to the exclusion list.
Windows 2000,XP,2003