No errors are generated
The Journal Mailbox is just a mailbox like any other mailbox so the EVPM script will disable archiving of the Journal Inbox as well.
This is expected behavior.
There are two options to prevent or correct this behavior.
1) Create a second EVPM script to zap the the Journaling mailbox and run it after running the original EVPM script followed by a synchronization of the journal mailbox
So: run original script, run script to zap mailbox, synchronize journal mailbox
2) Include a system default filter set to default for the journal mailbox
Refer Enterprise Vault Documentation, which will explain how a mailbox can be zapped using EVPM
Customer set up custom solution to archive specific folders and then runs an Enterprise Vault Policy Manager script to archive just those folders, and not archive the Inboxes. After the script is run, messages are no longer archived from the Journal Mailbox