An alternative method (I just realised) is to define the docked cell for the *Working* Screen Environment only
      
Cell[StyleData["Notebook", "Working"],DockedCells->{cells}]

Change the screen environment to *Presentation*, *Slideshow*, *Condensed* or *Printout* using *Format->Screen Environment* and then deploy / save as CDF via menu.  This method however will keep the docked cell in the CDF if the *Working* environment is deployed to CDF.