Yes, I have this problem too.
I also have a problem where after an IAA app has been removed from Cubasis, it's ports still appear in the MIDI port lists. As the app was opened and closed again in Cubasis there appears to be no app open on my iPad. To remove the port from the list I have to go and manually open the app outside of Cubasis and close it again. then it will be removed from the list of available ports in Cubasis. It's as though even though Cubasis is removing an app from an IAA slot it isn't properly closing the app down, but as no app is open outside of Cubasis you have no way of knowing it's still open so it just sits there (presumably putting a drain on your CPU). Is this a Cubasis problem that can be fixed in an update or is it a general IAA problem?
The problem happens a lot but I've noticed it with iMini, FunkBox and others.