In vista, when I boot clean, load any application ( Let's use IE as an example ),  then press Alt + Tab , I get 2 diffrent options to pick from. 1) My IE I now have open and 2) One labeled "Desktop".  My Current Dock bars number 2. One at the top, and one at the bottom of the screen.  When I select option 2 above, "Desktop", I get a clean window ( as expected ) with my top dock bar only.. My bottom one vanishes.

Any Ideas on what to look for?  THe top bar is tabbed, teh bottom one is not. I do not know if this makes a difference...