1. Check that the document library and contact is set to allow from all senders (network scanners were not regarded as authenticated users)
2. Check the size limits on the SharePoint send connector (Exchange -> Hub Transport -> Send Connectors -> Properties -> Maximum message size (KB))
3. Check the size limits on SMTP receiver on SharePoint (IIS 6 Mgr -> Properties on SMTP Virtual Server -> Messages tab -> Limit message size, Limit session size)
4. Turn off SharePoint reading RTF documents from Exchange (Exchange -> Hub Transport -> Remote Domains -> Format of original message sent as attachment to journal report: -> Exchange rich-text format -> Never use)
5. Check for potential mail routing problems (Exchange -> Hub Transport -> Accepted Domains -> Add domain for INTERNAL RELAY) – we noticed a couple of times the scanned mail tried to go external through our mail gateway – this was the last 1% of our problems.
Tips from: http://www.heyweb.net/2011/02/diagnosing-problems-with-sharepoint-incoming-email/