If the trailing spaces of your flat file message is being truncated by BizTalk then the workaround to this is add the (pad_char_type="none" ) attribute to the (schemainfo and fieldinfo) tags.I used the flat file schema wizard to generate the schema. Before modification my schema looked like this.
<xs:schema xmlns="” targetNamespace=" ">
<xs:annotation>
<xs:appinfo>
<b:schemaInfo standard="Flat File" codepage="65001" default_pad_char=" " pad_char_type="char" count_positions_by_byte="false" parser_optimization="complexity" lookahead_depth="3" suppress_empty_nodes="false" generate_empty_nodes="true" allow_early_termination="true" early_terminate_optional_fields="false" allow_message_breakup_of_infix_root="false" compile_parse_tables="false" root_reference="RecordNode" />
</xs:appinfo>
</xs:annotation>
<xs:element name="RecordNode">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" child_delimiter_type="hex" child_delimiter="0xD 0xA" child_order="postfix" sequence_number="1" preserve_delimiter_for_empty_data="true" suppress_trailing_delimiters="false" />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:annotation>
<xs:appinfo>
<b:groupInfo sequence_number="0" />
</xs:appinfo>
</xs:annotation>
<xs:element maxOccurs="unbounded" name="RecordField" type="xs:string">
<xs:annotation>
<xs:appinfo>
<b:fieldInfo justification="left" sequence_number="1" />
</xs:appinfo>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema
After modification my schema changed to this.
<xs:annotation>
<xs:appinfo>
<b:schemaInfo standard="Flat File" codepage="65001" pad_char_type="none" count_positions_by_byte="false" parser_optimization="complexity" lookahead_depth="3" suppress_empty_nodes="false" generate_empty_nodes="true" allow_early_termination="true" early_terminate_optional_fields="false" allow_message_breakup_of_infix_root="false" compile_parse_tables="false" root_reference="RecordNode" />
</xs:appinfo>
</xs:annotation>
<xs:element name="RecordNode">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" child_delimiter_type="hex" child_delimiter="0xD 0xA" child_order="postfix" sequence_number="1" preserve_delimiter_for_empty_data="true" suppress_trailing_delimiters="false" />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:annotation>
<xs:appinfo>
<b:groupInfo sequence_number="0" />
</xs:appinfo>
</xs:annotation>
<xs:element maxOccurs="unbounded" name="RecordField" type="xs:string">
<xs:annotation>
<xs:appinfo>
<b:fieldInfo justification="left" sequence_number="1" pad_char_type="none" />
</xs:appinfo>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>