This is with Snow Leopard. My Quick Entry Shortcut is set to Control-Space, but the issue still occurs even with other shortcuts (I tried Command-Shift-Comma and F13).
Clarification: If my main OmniFocus window is not hidden but obscured by other windows, invoking my Quick Entry shortcut brings just the Quick Entry window to the front as expected. However, if the main OmniFocus window is hidden (Command-H or OmniFocus -> Hide OmniFocus), invoking my Quick Entry shortcut brings both the main window and the Quick Entry window to the front with the Quick Entry window on top with keyboard focus.
Are you running the latest sneaky peak (r119278), Bill?