With POP3 the only interaction with the mail server is via the Inbox. Hence the Junk mail folder is just a local folder in your email client on your device.
When using IMAP then the folders in the online mailbox are synchronised to the email client. Normally, the email client would create a new set of folders to mirror those in the online mailbox.
Is your local Junk folder for Spam? Maybe that is now the Spam folder?
You'll see the standard folders via the Folder tree (Folder view selected) and any additional folders that can also be synchronised to your email client in the My Folders section below the standard folders.
Hi Andy142, it looks like Gondola's got you sorted. Please let us know how you get on.