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OK, experimenting a little more, I tried moving the Inspector window to Space 1 while leaving the rest of OmniFocus on Space 2. When I did this, if I opening OmniFocus from Space 1 using Quicksilver it doesn't switch me over to Space 2 (presumably because it finds an open OmniFocus window already on Space 1). Moving the Inspector to Space 2 (where the rest of my OmniFocus windows are) seems to resolve this.

Could this be related to what you're seeing?