Random skipping of MIDI notes is usually due to undersized MIDI buffer in "MIDI buffers, prepare using xx ms buffers". Double the buffer size, and that might fix it.
About that file with all notes locked, I don't know. If the clip is not locked, and the correct track is active, then I don't know what it could be. I don't know if it's possible to lock the MIDI-file itself uneditable. Even if the notes are outside the instruments key-range, the notes should still be editable.