Thanks Jeffrey! I removed "\n" from Separators and resolved the issue. 

@Jeffrey Drumm  and @Marc Mundt 
Thank you for your suggestions!

This setting allowed the X12 message to go to Epic... Batch Handling was set to "Whole Batch" and Framing on the BO to "Epic02/03" (Framing in BS was already set to "Flexible). 

Another issue that came up is the message is appearing in Epic with newlines after each segment. The Raw Contents in Iris Message Viewer (in the BS and BO) show the message without extra line in between segments. Does this mean Iris is sending the message without extra lines? Is there a setting in Iris that is adding the extra lines? BS setting Tolerate Newlines is true. 

Thanks again!
 

Hi Marc,

I tried "Whole Batch" and got the opposite from before. With this setting, the message is showing ISA header and 2 more segments (GroupDocsRef and IEA). It is "hiding" the rest. It is still not passing through the message.  

Message is changed to (1st picture). Clicking on Group documents "110" a second Group batch opens (2nd picture)

After clicking on TransactionSet documents "111", another section opens with the rest of the message. 

Is it possible to just pass through the message without hiding those sections? What settings do I need to do that?

Would Framing matter? It was set up as "Flexible" when Batch Handling was set up as "Whole Batch". 

Thank you!