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I fired up spaces, put OmniFocus in space 1 and OmniWeb in space 2, made the sidebar be about half the window width in OmniFocus, and switched back and forth repeatedly between the spaces via control->arrow keys with no apparent change to OmniFocus. Is that sufficient to cause the problem on your machine? What version of Mac OS X are you using? I tried quitting and restarting OmniFocus which also put my windows back exactly as they were.

I would try simplifying the problem a bit; if you open OmniFocus, resize the sidebar to suit, immediately quit OmniFocus and then relaunch it, do you get the window back as you left it?