Never noticed this one… I have two Apple Studio Displays ( 21 & 17 inches ) but I only plug one at a time to the MDD, so no dual display set-up here. The desktop picture differs from one to another due to the 21 inches' higher resolution, to my surprise when I use any of them, OS X does know which desktop I had which such display. How came that?, maybe the 17 inches' desktop picture behaves like being the 'by default' one and once I use the 21 inches such info is transmitted by the USB connection?, I highly doubt that…
Anyway, if OS X can know that… why wouldn't know the particular windows size for every app once opened with any of the displays? (*). I have to resize them since, -obviously- there is way more room on the 21 screen than the 17 model due to the former running at higher resolutions.
(*) I think that was accomplished by SwitchRes under OS 9, is it the same under OS X ?