[paulstone]

Do you have Mail.app open, and do you have the mail rule installed? Perhaps email that comes in is triggering the rule (which in turn will open up OmniFocus.

Or... is the the Quick Entry panel opening up at the same time as the main program? If it was, that would imply that there might be something like a keyboard shortcut triggering the Clipping/Inbox feature. You can check what it is currently set up to be in OmniFocus' preferences.

Hope that helps.
Paul.