… Ah, I thought things were going to well.
Got three InterApp audio tracks in my project; Nanologue, Arturia iSEM and DM1
Got “MIDI Input; Only for armed tracks” switched on in the settings.
Got MIDI data on each of the three tracks that I recorded using Cubasis’ on-screen keyboard with no problems.
It plays back fine, i.e. Each app plays the correct notes and mute/solo etc works as expected.
However, when I connect and play my MIDI keyboard, Arturia iSEM sounds even if I have not got its track selected or record armed. Arturia iSEM is not open, i.e. It’s not there when I double click the iPad’s home button. It’s just running in the IAA background like Nanolgue and DM1.
… Weird 
I get the feeling this whole IAA thing is still a bit of a flaky technology, and like you say Bry it’s probably down to Apple to develop it further and make it more robust.