I have observed some problems with startup behaviour of OmniFocus for some time now. I would like to share them, since I am not sure whether they are exactly a problem.
The issue looks following: when you shut down macOS with OF still open, it will be started again the following startup. However, OF seems to be not properly initialised in such a case. You can’t, for example, trigger the Quick Entry popup with a shortcut until you click the OF icon and force it to start properly. So, basically, it makes no difference whether OF starts up automatically or not - it will not work until you click the icon in the Dock.
In El Capitan the issue was different: a OF window would open in a startup which was completely unresponsive until you click the dock icon.
So, I am not sure whether it is my bad luck, interference with other tool installed or simply a problem in OF. Can someone confirm this issue?