It appears that when running Windows as a virtual machine in VMWare Fusion, (I’m using version 3.0.1), any windows programs that I am running with elevated permissions, (“run as administrator”), don’t appear in the OS X dock with Fusion in unity mode. What’s more, if I can see a portion of the window and I click it, it doesn’t come to the foreground.
My workaround for this, which worked very well, was to run Fusion in fullscreen mode in another Space. Then I was able to do my OS X testing in one space, flip to Windows to make changes very easily, (The default to move between spaces is ctrl + (arrow key), but I changed it to cmd + (arrow key) and it is much easier for me), and keep my E-mail & stuff open in a third space.
If you don’t have spaces active, in OS X 10.6 they’re in System Preferences > Exposé & Spaces > Spaces then just check the box that says “Enable Spaces” and adjust your shortcuts at the bottom of the window, if desired.