[Brian]

If you don't have a window open, we don't know which database to pull notifications from. As was mentioned in a previous post, you can have multiple OmniFocus databases.

Last time I discussed this with Ken, his suggestion was to leave a window open and use something like Spirited Away to hide OmniFocus when it's idle.

Edit: Huh, whaddaya know... looked this up in the feature request database, and it looks like there are plans to change it after all. Leaving the Spirited Away suggestion in place as a workaround for folks encountering this now.