Postbox 6 has changed how mails are stored. Here is an overview over what has changed: 

1. Instead of using /user/Library/Application Support/Postbox Postbox 6 now uses /user/Library/Application Support/PostboxApp . This means that any older version than Mail Archiver 4.2 beta 4 won't pick up the mailboxes from Postbox 6. 

2. Postbox 5 and older use the mbox format. For each mailbox folder there was one file containing all the mails in the mailbox. This gets cumbersome when you have large mailboxes. Postbox 6 uses what Mail has used since a very long time: one mail per file. This gives you a lot of files. But moving those files around when you move mails between mailboxes is a lot easier. 

You can select to use this new type of storage when you use Postbox the first time. The preferences setting in Advanced/General is for new accounts and doesn't change existing accounts.