[Toadling]

Erik, I don't think this is a bug you're seeing, but rather the result of design decisions made by Apple in Mac OS X. This snippet appears in Objective Development's LaunchBar Help file as a word of caution against running that app in the background without a Dock icon.

Yes, LaunchBar is a different kind of app, but I think much of this applies to OmniFocus as well:

In general, background applications are not considered to have a user interface or to become active. Thus be aware of the following shortcomings:

• Background applications do not appear in the Force Quit window. Instead you have to use Activity Monitor (or Process Viewer on Mac OS X 10.2) if you need to force quit LaunchBar.
  
• Background applications do not have their own menu bar. LaunchBar overcomes this problem by putting all the menu commands in the LaunchBar Action menu. This results in a quite large menu, though.
  
• Due to the missing menu bar, OS X displays the menu of the last active application, although this application is no longer active once you activate LaunchBar. This can be quite confusing. When you click in the menu, nothing happens (since the corresponding application isn't active), when you perform a menu shortcut, e.g. Command-Q, it will attempt to quit LaunchBar instead of the application displayed in the menu bar.
  
• Also due to the missing menu bar, the Hide Others command (Command-Option-H) will not work while LaunchBar is active. On Mac OS X there must be at least one foreground application that provides a menu bar. But if a background application - which has no own menu bar - hides all other applications, no menu bar would be left. Therefore OS X simply refuses to perform the Hide Others command when a background application is active.
  
• When running AppleScripts via LaunchBar, dialogs (such as used in the built-in Calculate script) cannot be confirmed with Return or Escape. You have to click the buttons with the mouse instead.
• Background applications are not notified, when you log out or shut down. Therefore you will not be asked to save any unsaved configuration changes.
  
• Background applications are not notified, when the keyboard layout did change. If the proper keyboard layout is set too late (e.g. during login, when LaunchBar is started automatically before the keyboard layout has been set), LaunchBar will use the wrong layout.
  
• The background mode can't be set individually on a per user basis. If LaunchBar is installed in a multi user environment, the modification will affect all users.

If these limitations still hold true for Leopard, which I believe they do, it seems like OmniFocus is not a very good candidate for a background application. Although, maybe it could work like iChat: Basic info shown in the Menu Bar with nothing in the Dock. Selecting an item in the Menu Bar, however, launches the full OmniFocus application with an icon in the Dock (like iChat launches when you select Buddy List).