I had exactly the same issue as Dave only yesterday regarding the iLok. Using Firefox4, iLok.com said I needed the latest drivers, but I'd only built this machine so I knew they were current and I had used iLok.com before on this machine... reinstalled them anyway, iLok.com still didn't work.
I did then try Safari and voila it worked, so realised it was a Firefox 4 issue. No biggie, transferred my new license over, done. Relaxed.
But something there messed with my AudioMidi preferences, and meant that OSX could see my 003 fine, but PT9 couldn't. Nice. Actually I have had this once before after upgrading to PT9, assumed it was just a random thing that happened. This time, I hadn't installed anything other than the iLok driver, but couldn't see how it was caused by that. I made a real mess though.. I re-ran the 003 Mac drivers (since PT9 installer doesn't have it inbuilt now, nice), plus the DioMidisomething driver that they also messed with the PT9.0.1 installer. Ran PT9, and it wouldn't even start now - OSX just said "this version of your software may not be compatible with this version of OSX (10.6.7), check with your vendor". At this stage, I was pretty happy. Started downloading 9.0.2 which timed out after an hour or so at ~40%, and wouldn't reconnect. Best day ever.
After much swearage, did the same googlefest, and finally fell over the delete the pref files idea to get them to rebuild.. and all appears to be back to norm. But now I am very suspicious this AudioMidi pref issue is something related to the iLok driver on OSX.. Thinking back, the 'random' time it happened before was just after I got my new machine, and I had just bought a new plugin to celebrate.
Did you re-install both of those iLok clients at some point in your panic Dave, or just one? I think I did both, maybe one of them should have a warning on it for 10.6.x
