[Toadling]

They do, at least on my system. Here's what I did to test:

1) Open a new OmniFocus window (sidebar hidden, toolbar hidden, view bar visible, resized to about a quarter of my screen size, position on the far right of my display).

2) With the new window in the front, select Perspective -> Save Window as New Perspective.

3) In the Perspectives window, I also ticked the "Always open in a new window" checkbox.

Now, whenever I open the saved perspective, the window appears exactly as I set it. Is this not the behavior you see?

-Dennis