If using an imap account then it is possible that it is not Thunderbird putting email into Spam. First we need to determine who is putting those emails into the Spam folder.

In the 'Spam' folder Make sure the 'Junk Status' column header is displaying. Are the junk flame icons a grey colour or a red/orange colour ? If they are grey then the server filter is putting the emails in the spam folder and thunderbird just displays it because it's a server folder - it shows what is on server. You would need to set up those emails as not spam via webmail account.

If the flame icons are coloured red/orange then it is Thunderbird marking as junk and putting emails into the designated Spam folder which in turn updates the server.

Please report back on what you see? Grey or coloured flame icon. Post image showing the Account Settings > 'Junk Settings' for the account. Disable this filter so it does not interfere whils testing - Set filters that move the mail back to the normal inbox either before or after the check.

Thank you so much - I haven't thought of the mails being preflagged as spam by the provider I use. I have disabled spam detection for the provider and now it works as it should.

Good to hear all is now ok.