is ths problem account on a different mail domain/server?

It may be the server admin has set the mail server to immediately delete "junk" or in the case of Yahoo they are deciding it should be in their bulk mail folder. Because when they decide is is spam that is where they put it and nothing you can do will change that.

Other accounts are on the same domain and server - all hosted by Rackspace. If I close Thunderbird and use the webmail interface to Rackspace, nothing gets deleted. In fact spam filtered by the rackspace filters doesn't even get deleted by Thunderbird, so it seems the problem only happens when Thunderbird actually moves the mail. I've also tried setting the account up in Outlook - no problems, behaves normally, but I really dislike Outlook.

Do you have filters on the account? that is one additional source of odd happenings when the logic in them is not quite right. Like delete instead of mark as junk.

Rackspace as I understand it are all Microsoft Exchange. is the "junk folder showing up as the Thunderbird junk folder name or the exchange Spam folder name. We might have a mismatch.

Thanks Matt,

I do have filters set, however they have been working for a few years. My Thunderbird at home is exactly the same set up with the same filters and all accounts work fine. I'll try removing them and see what happens.

There is a mismatch between the "junk" folder on Thunderbird and the "spam" folder on rackspace, but this has also been the case for years - and is also the case for the other accounts that work. When I reinstalled the account, I pointed Thunderbird to the rackspace spam folder, but exactly the same result.

I'll try doing a full reinstall of Thunderbird and see if the problem goes away. It's a puzzle!