Hey man,
Occasionally I get this when I flip back and forth from my External Interface and built in sound card... I sometimes also use my laptop with no interface connected and when I plug the interface back in I get this sort of thing...
I have fixed it a number of ways:
First of all I would recommend you delete all Pro Tools database files and preference files (this procedure works on all versions of PT 9 and 10 accept for 10.3.5 (latest release):
http://www.youtube.com/watch?v=Mj2fJHOz8GA
Once you have these databases deleted you can now make fresh ones by launching pro Tools, but hold down the N key until the playback engine window pops up... when it does make sure your presonus interface is selected as the default playback engine in the drop down menu at the top... now PT will replace all database/preferences files using this playback engines I/O, etc...
Now make sure the session overwrites existing I/O check box is not checked (so a session never overwrites your I/O setup).
This should have eliminated the I/O issues.
If not let me know and Ill give you an alternative way of fixing this.