In coherence in dual screen mode, Windows windows don't show where the osx menu bar would have been on the second screen had the menu bar been on that screen. I realize this can be worked around by altering the arrangement in displays preferences, but I prefer to keep the monitors side by side so windows are not offset when straddling screens. This is on the latest 3.0 build -- same prob was in the 2.x versions as well.
There is the Coherence limitation with dual-monitor configuration. The Windows screen should be rectangular for Coherence work. As the result you see unused area on the secondary screen.