I am not sure if this is application centric or Spaces centric, but often when I am switching between Spaces, the application that I switch to will not be brought to the forefront. For example, if I am going from a Finder window in Space 1 to a Word document in Space 2, when I switch to the Word document, though it will be highlighted (as if it were active), an inactive window in the same Space as the Word document will be on top of the Word document. I know that sounds convoluted, and I am having trouble recreating the issue so that I can take a picture and show you. Hopefully that made some sense! 