Mail problems after upgrading to Leopard 10.5.6

To day I upgraded my daughter's MacBook to Leopard 10.5.6 (from about 10.3 ?)
During the install the only problem was at the very end, the configuration wizard failed to make connection with the internet because Airport had lost the password for my wireless router. Once this had been reinserted we had instant internet connection, but by then I had closed the wizard.
Everything else went well except for Mail, the most important application!
When you click on Mail in the docking area it appears in the bar at the top of the screen but no window opens. To get one open we had to click on file> new viewer window. But this window was blank. Clicking on get new mail did nothing. No emails of any kind were visible. Checking the account details showed that they had transferred correctly, and the diagnostic window showed that it was connecting to the server and logging into the IMAP mail account OK.
Rebooting the Mac did not help.
The Mail program has to be forced to shut down, it won't exit gracefully.
I could not get it to send a message either, click "send" and it just sat there spinning its wheels.
At no point did we get any error messages.
We took a backup of the entire system to an external USB drive before the upgrade and all the files associated with Mail appear to be in the same place as before. There still seem to be hundreds of emails on file, we just can't see them. Clicking on one of there email files does nothing.
Is this a known problem? Is there some new feature of Mail we are not using? Has Mail failed to upgrade correctly? Any ideas how to fix this?
I've just found a note on theappleblog.com that suggests that Mailbox > Rebuild will solve this problem, but on this machine "Rebuild" is greyed out.

Hi,
Please note that this upgrade related problem would very likely be what has been covered by the support document at the link below:
http://support.apple.com/kb/TS2537
If you also find any files named to include MessageSorting (which would mean you once have upgraded from a version of OSX earlier than 10.4, which is clearly the case for you), remove those, also, but never restore those.
Often this is all that needs to be done, but you might then need to force an overall reindexing via the removal of the Envelope Index. Note the special instructions when forcing the reindexing of IMAP or Exchange accounts in the following:
http://docs.info.apple.com/article.html?path=Mail/3.0/en/14019.html
This will force the reindexing of all the POP mailboxes and all On My Mac mailboxes. With regard to any IMAP accounts if you have any, the practical result of this action of removing the account folder, is that with the IMAP account still set up in the Preferences, Mail will connect to the IMAP server and create a new account folder, and while doing so will index the messages in the mailbox folders of the IMAP accounts on the server.
Keep me posted.
Ernie

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