In Tools > Message Filters Do you have any Message Filters? Some people try to use the Message Filters for dealing with spam. This is not the best way of dealing with spam and you could end up with dozens if not hundreds of filters trying to deal with spam. Thunderbird built in Junk Controls when set up correctly and trained are really good at dealing with spam. Message Filters are best used for sorting good emails into various folders for organising. If you have any filters which have a Perform these actions set to move to trash or delete etc then disable them. Report back on whether this was the issue. In addition: Post info / image showing the junk settings for the account.