Import gives multiple copies of inbox

I've just started out with PortableApps (great idea and great software btw) but I've hit a problem with Thunderbird. I have a substantial Profile folder (lots of mails) from my 'full-fat' thunderbird installation and wanted to import that into Thunderbird Portable. I seem to have imported it OK in so far as the mails are in place and the accounts seem to have come across OK but I am seeing multiple (eight) 'Inbox' folders. If I click on any of them, I see the same content (i.e. my received mails!). I've had a search through the forum and haven't found anything that resembles this problem. I've also looked in all the places I can think of for .INI or other configuration files but no joy there either.

Can anybody give me some pointers on where to look or how to diagnose?

Cheers Steve