[Tim Wood]

Looking at this, my guess is that because OmniFocus is sending AppleEvents when running the script from the toolbar, it is busy doing its own thing when the system events process tries to ask it to perform UI actions.

Some of the other scripting support has 'suspend' support, but NSAppleScript doesn't... so fixing this looks like it might be relatively hard (at least I don't know the trick right off the top of my head).