In gmail, all emails that are received, sent and archived are in 'All Mail'. It is the global storage for gmail. Emails appear in other folders which gmail call labels because the 'label' is like a tag on an email in 'All Mail' which acts like a filter to faciliate the display of emails in other folders because users are used to that visual format. Gmail will also put new emails into other folders such as Important or Categories such as 'Social'. This can be a pain for those using POP as Thunderbird can only access and download from 'Inbox'. It is also a nuisance for those using IMAP because the folders in Categories are not allowed imap access. This is dictated by gmail not Thunderbird; you can see this in webmail account under 'Settings' > 'Settings' > 'Labels'. Suggest you logon to gmail webmail and see what you have got set up under 'Settings' > 'Configure Inbox'. I have only 'Primary' selected.