Hello,
Been there, done that :-)
There will always be messages that do not archive. I had several Journal Mailboxes having this, and I took below actions.
Create a new Journal Mailbox. Configure EV to archive from that mailbox (create a new task), to the same archive (or a new one). Change journal rule in Exchange to use the new Journal Mailbox. Verify items arrive into the new journal mailbox, then verify it archives items which come in.
Restart the task processing the old journal mailbox. Verify eventlog for events on this task/mailbox. It might be you see messages stating items cannot be archived, and cannot be moved to the 'failed' folders, and will be marked (are marked) as "do not journal". If you do see that, create a registry key: HKLM\Wow6432Node\KVS\Enterprise Vault\Agents DWORD ClearDoNotJournal value 1 when set, restart EV Services. Check to see if items are archived from that old mailbox. If not, change the value to 0, then restart services again.
Then remove the old Journal Mailbox from EV. Export the old Journal Mailbox to PST. Create a shared archive (as you cannot import into a Journal Archive...), in the same Vault Store as where your Journal Archives are. Import the PST file into the shared archive. If correct, all items will be imported.
Then you can delete the items from the old Journal Mailbox, or remove that alltogether.