For the record, there are indeed different spool formats. The standard mbox is a big, flat file. Life is much better when running maildir, which uses one file per message.
Would you do me a favor - would you cat out one of your individual message files and just verify that the message format looks like a normal flat message that gets parsed. Is there any funky added stuff, binary data, etc., or is it an unadulterated email message, just off by itself.
Thanks, Jale