To work around this problem, remove the root node child delimiter (set to none).
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Sample schema
<?xml version="1.0" encoding="utf-16"?>
<xs:schema xmlns="http://JunkA.SampleSchema" xmlns:b="http://schemas.microsoft.com/BizTalk/2003" targetNamespace="http://JunkA.SampleSchema" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:annotation>
<xs:appinfo>
<b:schemaInfo count_positions_by_byte="false" standard="Flat File" root_reference="Root" parser_optimization="complexity" />
<schemaEditorExtension:schemaInfo namespaceAlias="b" extensionClass="Microsoft.BizTalk.FlatFileExtension.FlatFileExtension" standardName="Flat File" xmlns:schemaEditorExtension="http://schemas.microsoft.com/BizTalk/2003/SchemaEditorExtensions" />
</xs:appinfo>
</xs:annotation>
<xs:element name="Root">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" preserve_delimiter_for_empty_data="true" suppress_trailing_delimiters="false" sequence_number="1" child_order="postfix" child_delimiter_type="char" child_delimiter="," />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:annotation>
<xs:appinfo>
<b:groupInfo sequence_number="0" />
</xs:appinfo>
</xs:annotation>
<xs:element name="Field1" type="xs:string">
<xs:annotation>
<xs:appinfo>
<b:fieldInfo sequence_number="1" justification="left" />
</xs:appinfo>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>