Hi mdwh2,
GUI components shouldn't change relative positions at all, so that the user doesn't have to hunt around to find them.
Unfortunately at the moment the scroll bars do need to be hunted and found. I would like them accessable at all times. If all windows on the left of the screen had their scroll bars on the right and vice a versa then there would be uniformity and it would be very obvious. If some windows had their scrollbars switched and some had not then, yes, it would be confusing as you suggest. I think that the default setting should be the centre of the Window/Palette. So a window being stretched from right to left would have the scrollbar jump from left to right.
Also, I think scroll bars are getting similiar to door handles, all shapes and sizes even different ways to use them but people figure them out pretty quickly.
OSX has areas that shift side of the main window and this does not confuse the user. This is heralded as a major feature of the email system and works very well.
I should have also added that scroll bars should move to be accessable if they are blocked by other objects.
Valan