I have Queue Pause from Presence box enabled. When setting my presence box to anything other than available, dialing into the queue produces results as expected, but dialing the extensions directly, it rings busy.
I thought it should just ring, or am I misunderstanding how this plugin works?
Or are you referring to presence box as something different as this:
The plugin "queue pause from presence" in itself does absolutely nothing but setting a queue member in pause.
Check that you might have other plugins that change device state (like presence DND), in that case, a custom device state is issued that might modify dialplan behaviour. But that is also totally dependant on your dialplan checking those states or not, something that is outside from FOP2 in itself.