Issue with XML file feel using Service Soap

We have a issue when processing the XML file feed (Java Input).There are a few Line items missing while processing the feed. However, when suppling directly from Pega (Service Soap), is able to capture all the line items (including the missing) and creates the work objects accordingly.

Note - there were no erorrs on the Tracer logs, also did logging for the this activity, no error found as well.