The only thing I notice in your settings that might be a problem is that the imap_folder_prefix has a trailing delimiter. I would change that to:

imap_folder_prefix = INBOX

I am not sure what folders you are wanting to see because the only folders I see in the command line output of your Maildir are the Sent, Draft, and Trash folders (the tmp,new and cur folders are part of the INBOX and the rest are courier specific files). What folders exactly are missing?

Thanks for the feedback,
Jason