It looks to me as though your problem is in fact the other way around. The layers have been absolutely positioned and are staying in the same place all the time while the rest of the content has been centred and moves with the screen resize.
When you use the favourites side bar you are just reducing the screen size etc. You would get the same effect if you dragged the right side of the screen over a bit.
I assume you want the layers to stay in a relative position to the rest of the content. One way to achieve this (without re-designing everything) is to construct a div around the whole content which you can centre and then apply a position relative to it. Which by inheritance will make the absolutely positioned divs/layers in your content absolutely positioned but relative to the position of the fluctuating new div. (does that make sense?).
Anyway something like this might work:
Put this style in-between the head tags on your page:
/*hack for IE5*/
Next you will need to surround your whole page with this class as follows. Start on the next line after the opening <body> tag and close the div the line before the closing</body> tag.
all your original body content goes here
With any luck this should sort your problem out