Not totally sure I understand your dilemma. But, might give this try, ok.
Move your pointer to an open area (no icons-shortcuts-ect.), of what you called "a huge-pane/window". Then hold your left mouse button down. Now, while holding the button down. Move the pointer to the bottom of the screen. Now release the mouse button. Are things back to the way you want them?
As I said, not sure of what you're describing.