How do I stop original emails in my inbox from duplicating to other folders?

I have 13 email accounts in Thunderbird. Most of the emails work flawlessly. However, in some accounts , before I read them, the original emails are "automatically" duplicated in other folders (for instance, "important", and or "save" folders). After reading the emails in my inbox, I have to open each folder where the duplicates are and wait for the emails to disappear "automatically". It's a pain b/c the folders are hi-lighted and therefore I can't tell if I received a new email in my inbox or is it an old one I just forgot to delete in another folder. How can I stop this from happening? Steps: 1. Email received in inbox; inbox high-lighted in blue 2. Open inbox in order to see emails, some folders (on the right-hand side) are also high-lighted in blue. The contain duplicates of emails in the inbox. 3. Deal with emails in inbox (open, read, keep, file, delete) 4. Some folders are still high-lighted in blue ( for instance, in uploaded image "all mail" and important") 5. Open high-lighted folders which deletes folders that were deleted in the inbox or if not deleted in the inbox, emails remain in the folder but the boldness turns off and the folder is no longer highlighted in blue. How do I stop the original emails from duplicating to other folders?