One thing to keep in mind with doing quota based archiving is the Mailbox task will only do one pass through your mailboxes. So you have to set your MaxNoofMsgsPerPass reg key large enough to ensure you are able to archive what you need on your mailboxes.
Location
HKEY_LOCAL_MACHINE
\SOFTWARE
\KVS
\Enterprise Vault
\Agents
Content
DWORD
Minimum: 200 (default)
Maximum: 10000
Description
Controls the maximum number of items that an Archiving Service will process per mailbox during a run. You may want to set this to a higher value if you use quota-based archiving, because then the Archiving Service stops after a single pass through all mailboxes.
However, note that it might be more efficient to modify the archiving rules to remove large items first, rather than reduce quota usage by increasing the number of items archived.
If you change this value you must restart each Archiving Service in order to use the new value.