Today all my account settings under Thunderbird where lost when I started it!
Everything seemed to be at the right place under C:\Documents and Settings\[myAccount]\Application Data\Thunderbird\Profiles\[a_number].default...
I discovered that there were a pref.js of 1 Ko and a prefs-1.js of 21 Ko (with all the aliases to my accounts)
Changing it and making Thunderbird point to the good location resolved the problem. But I don't know why it happended!
Looking at all the windows logs I found that yesterday night the automatic windows update installed this patch. I not sure it's it fault or someone hacked me...
Hope this won't happen again! (I'll start thinking of backuping this folder...)
A good page to resolve such issues can be found here.
update: another interesting link to manage/backup profiles informations.