Where have all my folders and emails gone on upgrade from 2 to 3

I am running thunderbird 2 on a 160gb usb hard drive.
I have about 100 folders in the Inbox plus 10 in my local folders each with sub folders.
I have 3.9GB of emails.

when it upgrades to 3 all I have is:-
Inbox(2608)
Inbox(11)
Drafts ....empty
Sent .....empty
Junk .....empty
Trash ... with 3 empty search folders
Outbox ...empty
Deleted ...empty
Folders ...empty should contain sub folders
Outlook Express Mail ...empty
Saved(653)
ZZZ folders ..empty should be about 30 sub folders

Where are all my folders and X times thousands emails?
How do I get them back

My address book is ok and all the message filters appear to be there.
My 15 accounts appears to be there.