Ok so 99.999% sure I've solved the problem for good now. But it wasn't easy... almost worse than a clean install.
Yesterday – earlier in the day I'd upgraded to Flash 11 and latest iTunes – I was in the process of...
1) Upgrading to iOS5
2) Upgrading also my Blackberry to OS6.0
When my Blackberry update crashed in the middle putting it into a locked or 'nuked' state as they say in Blackberry world.
As I frantically tried to fix this – online people were saying I needed to use Blackberry Desktop Manager on a PC / Parallels to get into it – but it also looked like I needed to update Blackberry Desktop Manager on the Mac to be able to get through to a nuked Blackberry like this. So I was trying out both at the same time! Anyway as I was in the process of launching Parallels and installing a new Blackberry Desktop Manager I noticed my system had suffered some kind of massive wipe out.
My address book was empty.
My calendar was empty.
After restoring the Blackberry (in the end the updated Blackberry Desktop Manger was sufficient to do this) I rebooted.
Now I saw it was even worse not only were all my contacts and calendars gone but all my system preferences too. All my settings, desktop backgrounds, email accounts, bookmarks etc. etc. completely gone.
I don't know precisely whether this occured during 1), 2) or when I was upgrading Blackberry Desktop Manager as I hadn't checked these apps before then.
Fortunately I was able to restore 90% of my data right away from MobileMe. Took a bit of figuring out because it turns out in Lion calendar syncing had moved to a different system control panel.
I say 90% of my data because I did loose some recent calendar dates that were not synced with MobileMe; but mostly it was all there.
I also think the MobileMe system preferences syncing completely failed. But it hasn't been too much trouble to set my desktop background again.
It was after I'd restored my bookmarks, calendars, contacts etc. all from MobileMe that I noticed that Lion was zipping along. Really as fast as Snow leopard had been if not faster. And way, way faster than any of my previous 'fixes' that I subsequently felt hadn't worked.
In the mood to upgrade (and having already stayed up to 11pm to get this far) I proceeded with the updates to iCloud (migrating my MobileMe), 10.7.2 (note my speed was fixed before this), iPhoto, iTunes. So far so good. All running really well. Syncs with iCloud vs MobileMe also appear to be much faster.
It's lovely to have my Mac back up to full speed again (without having to do a clean install) but looking back a clean install would probably have been a lot less stressful.
My hunch after all this experience is the cause for me was either:
a) Connected to some system preferences – so I could have just deleted all my system preferences for the same affect and started again.
b) Connected to my calendar, contacts or something within the categories of data supported by MobileMe that just needed a complete wipe out on the Mac and restore from the server to fix.
Hope this helps someone! I think a controlled backing up to the cloud (rather than my accidental); wiping locally; and then restoring could still be quicker to do than a clean install – I still didn't need to go through the pain of reinstalling CS5 etc.