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What is the exact B2B version you are working with?
When both are set in the body of the email, they both fail with document identification error.Either file is getting corrupted or identification details are incorrect. If possible, forward the logs in debug mode along with B2B configuration export and test data to my mail id (in my profile).
I tested your configuration with the payloads you sent and it is working for me. I used James Apache POP3 mail server and MS Outlook.
the xml file fails miserably as an attachment(SQL insert error while B2B tries to insert the wire information),Are you sure that there was no content in the body? If both mail body and attachment will have some content then you may see such errors because of a known bug. You may consider setting B2B EM property b2b.attachments.dir. This property holds the absolute directory name where B2B should store all incoming attachments. In case you will send a message with both body and attachment then attachment will be stored in the mentioned directory.
When both are set in the body of the email, they both fail with document identification error.For me both the payloads are working. Yes, the XML which you are using for testing is not correct as per the XSD you have uploaded in the document definition, but it won't affect processing as you have not enabled validation in the agreement.
Should we be able to receive an attachment either xml, or flat file or does it have to be within the body of the email?You should be able to receive message either as an attachment or in mail body. Both will work. If both body and attachment,both, will be present then usually body will be treated as a message (until body is too small in size)
So to debug the issue further, can you mail across the packed message (download it from wire message report) and transport headers. It seems the your mail server is adding some characters in the payload and that's why your B2B is failing.
You may also consider cleaning up your B2B repository once. take the backup of existing B2B configuration, purge the design time data (Administration --> Purge) and then import the configuration. I am asking for it because I saw few errors in your log which suggests that there may be some problem with MDS as well.
One more suggestion, I see that you have created a new document protocol "CustomXML". It is not required actually and you may create all your documents under existing document protocol "Custom" itself. However even if you use "CustomXML", there won't be any side effects.