Is the frame bigger or smaller than the window?
If you need to stretch the frame, then the Window Control object should do the job (I know you said you tried already, but I think you must have been doing something wrong).
If you need to shrink it to fit, then maybe the Viewport extension might work?
When you use the Window Control, are you using the Application Window actions or the Frame Window actions? You would want the Application Window actions, under Resize as opposed to Frame Window. Also, why would you change it during runtime? Why not by default? If you're planning on having it change for each level that could get both troublesome and annoying to the player...
Make sure that the window size set in the properties box, is bigger than your largest level (otherwise you'll get a border like you noticed) - you can just set it to some ridiculously huge size if you like.
Then, at the start of the frame, use the window control ("resize..." not "frame window...") to resize the view to the frame dimensions (from the storyboard controls).
And yeah, like Jon said - I don't think it's a good idea to resize the window between levels anyway. It would probably look better to just have your own decorative border to use up the empty space.