Mail.app using 80% CPU and won't quit - any ideas?

Hi, I'll try and cut a short story shorter...
I tried to begin using Mail.app last night instead of Entourage and Thunderbird just to see what it was like. Having never used mail.app before, I use the bundled import wizard to retrieve the settings from the Entourage account (POP, wifes ISP account) which seemed to work ok. I didn't test at this point as I have another account (POP again, my gMail) stored on Thunderbird which I also wanted to import.
To import the mailboxs from Thunderbird I copied the relevant folders from the ~\Library...\myprofile\... folder to the desktop and added the .mbox extension. Then used the import wizard 'other' option to bring them in.
All seemed to go ok. I recreated my 'other' account manually and sent/received some test mails etc. then marked everyting in all mailboxes as read.
At this point the laptop went very slow so I checked Activity Viewer - this showed Mail.app hovering between 70% - 80%. I thought this was a bit odd so I tried to Quit Mail, but it just hung. I then force quit and the CPU calms down.
I opened Mail again and it was ok for about 3 minutes until I try to view various mailboxes. Mail is still responsive but the mailboxes are empty! I use the rebuild function and they show the messages again, unless I look at a different one and then go back to the rebuilt mailbox - it's empty again.
Then the CPU/won't quit happened again. CPU is up at the same levels, Mail.app has 7 threads. I thought there may be some indexing going on so I went to bed. I got up this morning to find the G4 fans going crazy and CPU still consuming the CPU?
Any ideas?
I'm thinking I may trash both accounts and rebuild from scratch tonight.

Hi Ian.
Aside from whatever the problem is here (which I don't really know), you shouldn't add an .mbox extension to mbox files in order to import them into Mail. Mail uses that extension for something else. Also, you'd get better results using Eudora Mailbox Cleaner to do the conversion.

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