OK, so I'm not really sure what the values mean but I do see the zimbraPrefJunkLifetime is 0, although the Junk folder clears down about 75% of the stuff once a week or so, this means it's working to some extent. I haven't nailed down exactly when it's clearing.

Code:
root@mail:~# su zimbra
zimbra@mail:/root$ zmprov ga me@mydomain.com | grep -i Lifetime
zimbraAdminAuthTokenLifetime: 12h
zimbraAuthTokenLifetime: 2d
zimbraMailDumpsterLifetime: 30d
zimbraMailMessageLifetime: 0
zimbraMailSpamLifetime: 1d
zimbraMailTrashLifetime: 1d
zimbraPasswordLockoutFailureLifetime: 1h
zimbraPrefInboxReadLifetime: 0
zimbraPrefInboxUnreadLifetime: 0
zimbraPrefJunkLifetime: 0
zimbraPrefSentLifetime: 0
zimbraPrefTrashLifetime: 0