Hi, go to the main Library folder on your HD (not you user Library folder) and then Audio > MIDI Drivers. Remove the DigiDioMIDI.plugin driver that Pro Tools installed there. You won't need it as it an old digidesign driver for old Digidesign gear, and it happens to mess with Core MIDI as you've witnessed for yourself.
Mac mini i7 2.3 GHz - 16GB RAM | OS 10.9.2 | Logic Pro 10.0.6 |
MacBook Pro 15" Core 2 Duo 2.2 GHz - 6GB RAM | OS 10.6.8 | Logic Pro 9.1.8 |
RME Fireface 400 | Akai MPK49 | Nord Micro Modular |