After the iTunes update and a Restart, I opened DP and got a message saying that the Audio Hardware Setup had changed and that DP would open without Audio! Yikes.
I looked in System Preferences>Sound and was gobsmaked to see only my iSight camera. No other audio devices at all. No Built In, no digital, no USB, no Firewire devices.
Next I looked in Audio/MIDI Setup and again only the iSight camera on the Audio Window. The MIDI Window was empty apart from a "LOADING" message. And the spinning beachball. AMS then seemed to lock up. I could not switch windows nor could I switch to other open applications. I finally got the cursor's Pointer tool back via the Dock and Forced AMS to Quit.
I did a quick cable check, re-plugging all my audio devices and then checked About This Mac>System Report. This showed all my connected USB and Firewire devices were being recognised on the relevant busses EXCEPT my MOTU 828II FW and my MTP AV usb. Both appeared as Unidentified Device.
After a few restarts and finally disconnecting the 828, I have finally got my Firewire devices to show up in System Prefs and AMS, BUT AMS still locks once it is opened, and the MIDI Window is intermittently showing connected devices with a red question mark superimposed on their icons, OR it's the empty window with "LOADING". iTunes will not begin playback of any selected tracks.
I have a call scheduled with Apple Support at 14.45 GMT. I have Time Machine backups which could re-instate the system to its last working state, but I'd like some guidance from Apple before I undertake that.
My MacBook Pro also has iTunes 10.4.1 and USB and Firewire audio devices attached. Everthing on that system works fine, so this COULD be a problem which primarilty affects MOTU hardware - my Firewire devices were daisychained with the 828 in the chain, and my MTP AV is the hub for most (but not all) of my MIDI devices.
I'll report back after the call with Apple. Meantime, if you run a recent Mac Pro AND Lion, think carefully before installing iTunes 10.4.1.

Mike