In such cases, we could try Debug or Check each output Stages with the help of Immediate Panel or Writing the Serialized text of the output to a text file.
Also, if it is possible we would like to also test the same case at our end if provided with the two sample documents.
When also mentioned identical in all aspects, we would also need to know How many documents were trained if using the DU Model or with ML Skill. We would like to know what was the ML Package used.