Like Nitass mentioned here, do you have recipient validation enabled? If so are you dropping messages to invalid recipiets using LDAP Sync, or rejecting messages to invalid recipients with a recipient validation source?
If dropping messages using LDAP Sync, you need to make sure LDAP Syncronization and Scanner Replication occur before messages will be accepted to the new recipient.
Have you enabled the message audit logs and what is it reporting has happend to the messages?
Kevin