It could be part of your problem. Make sure you have the
latest drivers installed for your Presonus interface. Next make sure you see the Audiobox listed in your Mac Audio Devices. It should not be part of the Pro Tools Agregate.
Launch PTF and hold down the N key while it loads which will bring you to the Playback Engine when it loads. You should now see the Presonus interface in the list and should be able to select it. If all goes well, you will be able to add a track to a new session and be able to choose from the inputs/outputs on the Audiobox.