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I want to archive the many 100s of emails in folders on my IMAP account using Thunderbird. I was able to do it for one folder earlier, but now T-bird is only downloading 1-2 messages per folder.

Any thoughts on how to get all 100+?

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would be nice to provide at least some info about mail provider (gmail etc.). If you can connect to your mailbox using webmail, then try to set all those messages as unread and then try to get them in TB again. – Juhele Mar 28 '12 at 6:35

Under Account Settings -> Synchronization & Storage you will see all the options around offline synchronization.

It will have settings to allow you to specify to synchronize X number of recent emails per folder. You can also configure which folders you want to synchronize (ie, you probably don't want to sync the SPAM folder.

If your version of Thunderbird doesn't have these options, go and grab 12.01.

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