I fixed this by overriding Evince's window size in my window manager. If you're using compiz, open the configuration tool (ccsm) and go to Window Management > Window Rules then create a new size rule for Evince (Type set to Class; you can use the window selector to set the Class to Evince by clicking on an open Evince window). I set mine to 1000x600, and it works nicely. You can see Evince set it's default size on startup (off-screen, as I also have a dual monitor setup with differing resolutions), but then the window manager forces the size rule and sets it to what you want.
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