Certain BeOS utilities that run in all workspaces will grab focus when you switch between workspaces (the excellent DeposIt launcher, for example). This means that when you switch back to the original workspace, you’ll have to click in the app you were last using to bring it back to the front.
While you can disable this annoying behavior by setting DeposIt (or whatever) to run only in a single workspace, a better solution is to install hey and put this in your UserBootscript after the app has been launched:

hey DeposIt set Flags of Window 0 to 208 &

Want to know where we got the number 208? See the tip Control window look, feel, or behavior with „hey“.