During the mail copy process, folders which contain no mail are not created as labels on Titan Apps email. Any sub-folders are created, though, and your label list may end up looking like this:
Note how there was an Important Mail folder containing 4 sub-folders, however they are not shown nested correctly. There is a simple fix to correct this: Create a new label with the name of the parent folder which was empty. To do so, scroll to the bottom of the label list, click More, and choose "Create New Label." Give it the same name as the missing folder, in this case Important Mail.
Mail will automatically collapse the labels into this one and it will now show up as expected, as show here: