I believe manual Archive is working on the Received date with messages that were not previously flagged - but I'll double check.
Do Not AutoArchive is not checked in Properties on these messages, but I'll try checking the box in Archive settings to include those anyway.
My client is running Outlook 2007 SP3. We recently made the registry change to allow Archiving to use the Received date instead of the Modified date (ArchiveIgnoreLastModifiedTime).
After the registry change, his Inbox count went down from 15,000 messages to 8,000 - a good start.