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You pretty much have to have the Restore: Layout box checked on everything...or have the ones with different layouts have the "Alway open in new window" box checked. Otherwise, as soon as the window gets adjusted by a perspective that restores the layout to a saved value, any subsequent perspectives invoked that don't have Restore: Layout checked will get the window as it was when you summoned the perspective. Another way of looking at it is that there isn't a default setup that the window "snaps back" to every time you go to a perspective that doesn't have Restore: Layout checked.

I'll also say that in my experience, the Restore: Layout code often gets it wrong when asked to resize windows and hide/show the toolbar. If something seems broken, it might be!