Hello,
Indeed Pro Tools f*cked up my MIDI configuration on my brand new iMac (which came with OS X 10.7 installed).
I have an USB Midi keyboard that worked fine with apps like Sibelius or Garage band. After installing Pro Tools 8.0.5, the MIDI keyboard works within Pro Tools but it can't be seen by any other application. And the Mac MIDI configuration tool tells me something like "Core MIDI server crashed blah blah".
Also tested with another keyboard attached to the Midi port of the Mbox 2. Same results: the keyboard is ok within Pro Tools but can't be used by any other application.
To sum up, Pro Tools itself works but it prevents other applications to work
