You're likely archiving your messages via a scheduled COS job, and selecting them by SourceConfigName and TargeteConfigName. The returned ACKs, although objects of class EnsLib.HL7.Message and stored in the same message store, don't have those properties so they're not going to show up.
You could modify the job so that for each message fetched, select from Ens.MessageHeader where the OriginalDocId is the ObjectId of the sent message; that should get you access to the ACK's ObjectId so you can open and fetch the ACK message.
You could also extend the HL7.Adapter.TCPOutboundAdapter's HL7Message() method to log the outbound message and its ACK to a file in realtime, rather than using a scheduled job.
Jeff Drumm
HICG, LLC