Symptom
Mail does not display new mailbox folders that you added to an IMAP account. However, the mailbox folders appear as an option in the Transfer submenu of the Message menu.
Solution
You may resolve this by creating an additional, dummy account.
1. Choose Preferences from the Mail menu.
2. Click Accounts, if necessary.
3. Click Add Account.
4. Configure the account with dummy (bogus, fake) information. It does not matter if the account is POP or IMAP.
Note: You should deselect the Advanced tab option "Include when automatically checking for new mail".
5. Click OK.
6. Close the Mail Preferences window.
7. Try creating new mailbox folders. If they do not appear, then quit and reopen Mail.
Figure 1 shows how this might look. Click the disclosure triangle to the left of the account name (or location) to see subfolders.
Figure 1 Mailbox folders