The internal BOM generator has bugs. I designed an XSL script, which converts...

if(UNIX)

# Install the *.xsl file(s), user will need to install 'xsltproc' and setup

    add_definitions(-D__UNIX__)

# EESCHEMA's netlist plugins

endif(UNIX)

# See chapter 14 of eeschema.pdf

# add_executable(netlist_form_pads-pcb netlist_form_pads-pcb.cpp)

# install(TARGETS netlist_form_pads-pcb   DESTINATION ${KICAD_PLUGINS}  COMPONENT binary)

# install the *.xsl file(s), user will need to install 'xsltproc' and setup

set( xsl_lst

# EESCHEMA's netlist plugins

    bom2csv.xsl

install( FILES

    bom_cvs.xsl

    netlist_form_cadstar-RINF.xsl

    netlist_form_cadstar.xsl

    netlist_form_OrcadPcb2.xsl

    netlist_form_pads-pcb.xsl

    netlist_form_pads-pcb.xsl

    )

install( FILES ${xsl_lst}

    DESTINATION ${KICAD_PLUGINS}

    DESTINATION ${KICAD_PLUGINS}

    COMPONENT binary

    COMPONENT binary

    )

    )

<!--XSL style sheet to convert EESCHEMA XML Partlist Format to CSV BOM Format

    Copyright (C) 2013, Stefan Helmert.

    GPL v2.

    Functionality:

        Generation of csv table with table head of all existing field names

        and correct assigned cell entries

    How to use this is explained in eeschema.pdf chapter 14.  You enter a command line into the

    netlist exporter using a new (custom) tab in the netlist export dialog.  The command is

    similar to

        on Windows:

            xsltproc -o "%O.csv" "C:\Program Files (x86)\KiCad\bin\plugins\bom2csv.xsl" "%I"

        on Linux:

            xsltproc -o "%O.csv" /usr/local/lib/kicad/plugins/bom2csv.xsl "%I"

    Instead of "%O.csv" you can alternatively use "%O" if you will supply your own file extension when

    prompted in the UI.  The double quotes are there to account for the possibility of space(s)

    in the filename.

-->

<!DOCTYPE xsl:stylesheet [

  <!ENTITY nl  "&#xd;&#xa;">    <!--new line CR, LF, or LF, your choice -->

]>

<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">

    <xsl:output method="text"/>

    <!-- for table head and empty table fields-->

    <xsl:key name="headentr" match="field" use="@name"/>

    <!-- main part -->

    <xsl:template match="/export">

        <xsl:text>Reference, Value, Footprint, Datasheet</xsl:text>

            <!-- find all existing table head entries and list each one once -->

            <xsl:for-each select="components/comp/fields/field[generate-id(.) = generate-id(key('headentr',@name)[1])]">

                <xsl:text>, </xsl:text>

                <xsl:value-of select="@name"/>

            </xsl:for-each>

            <xsl:text>&nl;</xsl:text>

        <!-- all table entries -->

        <xsl:apply-templates select="components/comp"/>

    </xsl:template>

    <!-- the table entries -->

    <xsl:template match="components/comp">

        <xsl:value-of select="@ref"/><xsl:text>,</xsl:text>

        <xsl:value-of select="value"/><xsl:text>,</xsl:text>

        <xsl:value-of select="footprint"/><xsl:text>,</xsl:text>

        <xsl:value-of select="datasheet"/>

        <xsl:apply-templates select="fields"/>

        <xsl:text>&nl;</xsl:text>

    </xsl:template>

    <!-- table entries with dynamic table head -->

    <xsl:template match="fields">

        <!-- remember current fields section -->

        <xsl:variable name="fieldvar" select="field"/>

        <!-- for all existing head entries -->

        <xsl:for-each select="/export/components/comp/fields/field[generate-id(.) = generate-id(key('headentr',@name)[1])]">

            <xsl:variable name="allnames" select="@name"/>

            <xsl:text>,</xsl:text>

            <!-- for all field entries in the remembered fields section -->

            <xsl:for-each select="$fieldvar">

                <!-- only if this field entry exists in this fields section -->

                <xsl:if test="@name=$allnames">

                    <!-- content of the field -->

                    <xsl:value-of select="."/>

                </xsl:if>

                <!--

                    If it does not exist, use an empty cell in output for this row.

                    Every non-blank entry is assigned to its proper column.

                -->

            </xsl:for-each>

        </xsl:for-each>

    </xsl:template>

 </xsl:stylesheet>