MIDI crash, PT now unable to communicate with controller

[jes]

A set of problems has left PT9 unable to communicate with my Axiom 61 (first gen).
First, I was using Melodyne to analyze a bass guitar track, transferred it and it was fine. Then I selected "save as MIDI file", and it failed and crashed PT.
So I reopened PT, the session, tried it all again and it managed to save the file, but crashed PT again.
Reopened the session, imported the new midi track to new track, but PT now says its run out of memory and can't save the session (16GB ram, here, on a MAC PRO, at least 1TB of free disk space.)
Rebooting, opened PT, and now I discover that no instrument tracks receive midi from the keyboard. Adding the Axiom as a Midi controller, i get the endless "Pro Tools is unable to communicate with M-Audio Axiom 61" etc...

A midi track set to have the keyboard as input will receive midi. An instrument track (no way to set midi input) will not. An instrument track with midi information on the track will not play these notes, appears blued out somehow?

What's going on here?