Customized CQWP display only multiple columns after migration to 2013 when source is a list.

If I select Show items from all sites in this site collection or Show items from the following site and all subsites as Query source all my custom columns are with out value, if I select Show items from the following list every thing is as it should be.
(Se picture)
This is show multiple columns values correctly:
<webParts>
  <webPart xmlns="http://schemas.microsoft.com/WebPart/v3">
    <metaData>
      <type name="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
      <importErrorMessage>Cannot import this Web Part.</importErrorMessage>
    </metaData>
    <data>
      <properties>
        <property name="Filter1ChainingOperator" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterChainingOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">And</property>
        <property name="FilterOperator1" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="Direction" type="direction">NotSet</property>
        <property name="FilterOperator3" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="GroupByDirection" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+SortDirection, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">Asc</property>
        <property name="DataSourceID" type="string" />
        <property name="ChromeState" type="chromestate">Normal</property>
        <property name="SystemViewFields" type="string" />
        <property name="ListName" type="string">Document library</property>
        <property name="FilterDisplayValue3" type="string" />
        <property name="FilterDisplayValue2" type="string">5.7.2</property>
        <property name="FilterDisplayValue1" type="string">HCM/Payroll</property>
        <property name="FilterField1" type="string">SectionName</property>
        <property name="Description" type="string">Use to display a dynamic view of content from your site on a web page</property>
        <property name="DataColumnRenames" type="string" />
        <property name="MissingAssembly" type="string">Cannot import this Web Part.</property>
        <property name="PageSize" type="int">-1</property>
        <property name="ViewContentTypeId" type="string" />
        <property name="ParameterBindings" type="string" null="true" />
        <property name="HelpUrl" type="string" />
        <property name="AdditionalFilterFields" type="string" />
        <property name="DataMappingViewFields" type="string">{fa564e0f-0c70-4ab9-b863-0177e6ddd247},Text;</property>
        <property name="Title" type="string">Prod CQWP</property>
        <property name="FeedDescription" type="string" />
        <property name="UseCache" type="bool">True</property>
        <property name="XslLink" type="string" null="true" />
        <property name="AutoRefresh" type="bool">False</property>
        <property name="Filter1IsCustomValue" type="bool">False</property>
        <property name="FireInitialRow" type="bool">True</property>
        <property name="FilterValue3" type="string" />
        <property name="SortByFieldType" type="string">DateTime</property>
        <property name="ManualRefresh" type="bool">False</property>
        <property name="HelpMode" type="helpmode">Modeless</property>
        <property name="AllowConnect" type="bool">True</property>
        <property name="ItemStyle" type="string">DesignDocumentsTest</property>
        <property name="SampleData" type="string">&lt;dsQueryResponse&gt;
                    &lt;Rows&gt;
                        &lt;Row Title="Item 1" LinkUrl="http://Item1" Group="Group Header" __begincolumn="True"
__begingroup="True" /&gt;
                        &lt;Row Title="Item 2" LinkUrl="http://Item2" __begincolumn="False" __begingroup="False"
/&gt;
                        &lt;Row Title="Item 3" LinkUrl="http://Item3" __begincolumn="False" __begingroup="False"
/&gt;
                    &lt;/Rows&gt;
                    &lt;/dsQueryResponse&gt;</property>
        <property name="FilterIncludeChildren2" type="bool">False</property>
        <property name="XmlDefinitionLink" type="string" />
        <property name="ServerTemplate" type="string">101</property>
        <property name="TitleUrl" type="string" />
        <property name="CommonViewFields" type="string">Title,Text;Product_x0020_Name,Choice;Areabranch,Choice;ProdcutDesignDocCategory,Choice;User_x0020_Story,Text;Status,Choice</property>
        <property name="QueryOverride" type="string" />
        <property name="DataSourcesString" type="string" />
        <property name="DisplayName" type="string" />
        <property name="ListGuid" type="string">ce5f8d8e-6ab9-4ed1-8c10-557362473348</property>
        <property name="DataFields" type="string" />
        <property name="ShowWithSampleData" type="bool">False</property>
        <property name="GroupByFieldType" type="string">Choice</property>
        <property name="Default" type="string" />
        <property name="ViewFlags" type="Microsoft.SharePoint.SPViewFlags, Microsoft.SharePoint, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">None</property>
        <property name="ContentTypeBeginsWithId" type="string">0x010100634C5EFE866C834E92467F3F8D9C37C7080401</property>
        <property name="AllowHide" type="bool">True</property>
        <property name="FeedEnabled" type="bool">False</property>
        <property name="SortBy" type="string">Modified</property>
        <property name="FilterByContextTerm" type="bool">False</property>
        <property name="TitleIconImageUrl" type="string" />
        <property name="PlayMediaInBrowser" type="bool">True</property>
        <property name="ViewFlag" type="string">0</property>
        <property name="Xsl" type="string">&lt;xsl:stylesheet xmlns:x="http://www.w3.org/2001/XMLSchema" version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:cmswrt="http://schemas.microsoft.com/WebPart/v3/Publishing/runtime" exclude-result-prefixes="xsl cmswrt x" &gt; &lt;xsl:import href="/Style Library/XSL Style Sheets/Header.xsl" /&gt; &lt;xsl:import href="/Style
Library/XSL Style Sheets/ItemStyle.xsl" /&gt; &lt;xsl:import href="/Style Library/XSL Style Sheets/ContentQueryMain.xsl" /&gt; &lt;/xsl:stylesheet&gt;</property>
        <property name="FilterField2" type="string">Product_x0020_Version</property>
        <property name="ChromeType" type="chrometype">TitleOnly</property>
        <property name="CacheXslTimeOut" type="int">86400</property>
        <property name="AdditionalGroupAndSortFields" type="string" />
        <property name="UseSQLDataSourcePaging" type="bool">True</property>
        <property name="Height" type="string" />
        <property name="DataMappings" type="string">User_x005F_x0020_Story:|LinkUrl:|Description:|OpenInNewWindow:|Product_x005F_x0020_Name:|Areabranch:|ImageUrl:|Title:{fa564e0f-0c70-4ab9-b863-0177e6ddd247},Title,Text;|LinkToolTip:|ProdcutDesignDocCategory:|Status:|SipAddress:|</property>
        <property name="ListUrl" type="string" null="true" />
        <property name="ShowUntargetedItems" type="bool">False</property>
        <property name="AllowMinimize" type="bool">True</property>
        <property name="GroupBy" type="string">Areabranch</property>
        <property name="FilterIncludeChildren1" type="bool">False</property>
        <property name="BaseType" type="string" />
        <property name="MainXslLink" type="string" />
        <property name="AsyncRefresh" type="bool">False</property>
        <property name="FilterValue1" type="string">HCM/Payroll</property>
        <property name="FilterValue2" type="string">5.7.2</property>
        <property name="InitialAsyncDataFetch" type="bool">False</property>
        <property name="AutoRefreshInterval" type="int">60</property>
        <property name="Filter3IsCustomValue" type="bool">False</property>
        <property name="GroupStyle" type="string">Band</property>
        <property name="AllowZoneChange" type="bool">True</property>
        <property name="FilterIncludeChildren3" type="bool">False</property>
        <property name="EnableOriginalValue" type="bool">False</property>
        <property name="ItemLimit" type="int">3</property>
        <property name="FilterType1" type="string">Choice</property>
        <property name="UseCopyUtil" type="bool">True</property>
        <property name="FilterType3" type="string" />
        <property name="FilterType2" type="string">Choice</property>
        <property name="FilterOperator2" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="PageType" type="Microsoft.SharePoint.PAGETYPE, Microsoft.SharePoint, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">PAGE_NORMALVIEW</property>
        <property name="FilterByAudience" type="bool">False</property>
        <property name="ItemXslLink" type="string" />
        <property name="Hidden" type="bool">False</property>
        <property name="WebUrl" type="string">~sitecollection/ProductDevelopment/HCMPayroll/HRMSproject572</property>
        <property name="HeaderXslLink" type="string" />
        <property name="CacheXslStorage" type="bool">True</property>
        <property name="ListsOverride" type="string" />
        <property name="SortByDirection" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+SortDirection, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">Asc</property>
        <property name="Filter2IsCustomValue" type="bool">False</property>
        <property name="AllowEdit" type="bool">True</property>
        <property name="FeedTitle" type="string" />
        <property name="FilterField3" type="string" />
        <property name="MediaPlayerStyleSource" type="string" null="true" />
        <property name="DisplayColumns" type="int">2</property>
        <property name="Filter2ChainingOperator" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterChainingOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">And</property>
        <property name="XmlDefinition" type="string" />
        <property name="WebsOverride" type="string" />
        <property name="AllowClose" type="bool">True</property>
        <property name="ContentTypeName" type="string" />
        <property name="ListId" type="System.Guid, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089">00000000-0000-0000-0000-000000000000</property>
        <property name="ExportMode" type="exportmode">All</property>
        <property name="NoDefaultStyle" type="string" null="true" />
        <property name="ViewFieldsOverride" type="string" />
        <property name="CatalogIconImageUrl" type="string" />
        <property name="ListDisplayName" type="string" null="true" />
        <property name="Width" type="string" />
      </properties>
    </data>
  </webPart>
</webParts><label for="ctl00_MSOTlPn_EditorZone_Edit0g_789619b5_3406_469e_8b24_fc42ff130ea0_CBQToolPartshowItemsFromListRadioButton"></label>
This is with missing columns values
<webParts>
  <webPart xmlns="http://schemas.microsoft.com/WebPart/v3">
    <metaData>
      <type name="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
      <importErrorMessage>Cannot import this Web Part.</importErrorMessage>
    </metaData>
    <data>
      <properties>
        <property name="Filter1ChainingOperator" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterChainingOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">And</property>
        <property name="FilterOperator1" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="Direction" type="direction">NotSet</property>
        <property name="FilterOperator3" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="GroupByDirection" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+SortDirection, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">Asc</property>
        <property name="DataSourceID" type="string" />
        <property name="ChromeState" type="chromestate">Normal</property>
        <property name="SystemViewFields" type="string" />
        <property name="ListName" type="string" />
        <property name="FilterDisplayValue3" type="string" />
        <property name="FilterDisplayValue2" type="string">5.7.2</property>
        <property name="FilterDisplayValue1" type="string">HCM/Payroll</property>
        <property name="FilterField1" type="string">{a10809c0-a375-4279-ade5-2603dbdcd7e9}</property>
        <property name="Description" type="string">Use to display a dynamic view of content from your site on a web page</property>
        <property name="DataColumnRenames" type="string" />
        <property name="MissingAssembly" type="string">Cannot import this Web Part.</property>
        <property name="PageSize" type="int">-1</property>
        <property name="ViewContentTypeId" type="string" />
        <property name="ParameterBindings" type="string" null="true" />
        <property name="HelpUrl" type="string" />
        <property name="AdditionalFilterFields" type="string" />
        <property name="DataMappingViewFields" type="string">{fa564e0f-0c70-4ab9-b863-0177e6ddd247},Text;</property>
        <property name="Title" type="string">Prod 1 Lib CQWP</property>
        <property name="FeedDescription" type="string" />
        <property name="UseCache" type="bool">True</property>
        <property name="XslLink" type="string" null="true" />
        <property name="AutoRefresh" type="bool">False</property>
        <property name="Filter1IsCustomValue" type="bool">False</property>
        <property name="FireInitialRow" type="bool">True</property>
        <property name="FilterValue3" type="string" />
        <property name="SortByFieldType" type="string">DateTime</property>
        <property name="ManualRefresh" type="bool">False</property>
        <property name="HelpMode" type="helpmode">Modeless</property>
        <property name="AllowConnect" type="bool">True</property>
        <property name="ItemStyle" type="string">RDDesignDocuments</property>
        <property name="SampleData" type="string">&lt;dsQueryResponse&gt;
                    &lt;Rows&gt;
                        &lt;Row Title="Item 1" LinkUrl="http://Item1" Group="Group Header" __begincolumn="True"
__begingroup="True" /&gt;
                        &lt;Row Title="Item 2" LinkUrl="http://Item2" __begincolumn="False" __begingroup="False"
/&gt;
                        &lt;Row Title="Item 3" LinkUrl="http://Item3" __begincolumn="False" __begingroup="False"
/&gt;
                    &lt;/Rows&gt;
                    &lt;/dsQueryResponse&gt;</property>
        <property name="FilterIncludeChildren2" type="bool">False</property>
        <property name="XmlDefinitionLink" type="string" />
        <property name="ServerTemplate" type="string">101</property>
        <property name="TitleUrl" type="string" />
        <property name="CommonViewFields" type="string">Title,Text;Product_x0020_Name,Choice;Areabranch,Choice;ProdcutDesignDocCategory,Choice;User_x0020_Story,Text;Status,Choice</property>
        <property name="QueryOverride" type="string" />
        <property name="DataSourcesString" type="string" />
        <property name="DisplayName" type="string" />
        <property name="ListGuid" type="string" />
        <property name="DataFields" type="string" />
        <property name="ShowWithSampleData" type="bool">False</property>
        <property name="GroupByFieldType" type="string">Text</property>
        <property name="Default" type="string" />
        <property name="ViewFlags" type="Microsoft.SharePoint.SPViewFlags, Microsoft.SharePoint, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">None</property>
        <property name="ContentTypeBeginsWithId" type="string">0x010100634C5EFE866C834E92467F3F8D9C37C7080401</property>
        <property name="AllowHide" type="bool">True</property>
        <property name="FeedEnabled" type="bool">False</property>
        <property name="SortBy" type="string">{28cf69c5-fa48-462a-b5cd-27b6f9d2bd5f}</property>
        <property name="FilterByContextTerm" type="bool">False</property>
        <property name="TitleIconImageUrl" type="string" />
        <property name="PlayMediaInBrowser" type="bool">True</property>
        <property name="ViewFlag" type="string">0</property>
        <property name="Xsl" type="string">&lt;xsl:stylesheet xmlns:x="http://www.w3.org/2001/XMLSchema" version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:cmswrt="http://schemas.microsoft.com/WebPart/v3/Publishing/runtime" exclude-result-prefixes="xsl cmswrt x" &gt; &lt;xsl:import href="/Style Library/XSL Style Sheets/Header.xsl" /&gt; &lt;xsl:import href="/Style
Library/XSL Style Sheets/ItemStyle.xsl" /&gt; &lt;xsl:import href="/Style Library/XSL Style Sheets/ContentQueryMain.xsl" /&gt; &lt;/xsl:stylesheet&gt;</property>
        <property name="FilterField2" type="string">{d51bf689-5b9f-454b-9d6a-4e2c375ec3fe}</property>
        <property name="ChromeType" type="chrometype">TitleOnly</property>
        <property name="CacheXslTimeOut" type="int">86400</property>
        <property name="AdditionalGroupAndSortFields" type="string" />
        <property name="UseSQLDataSourcePaging" type="bool">True</property>
        <property name="Height" type="string" />
        <property name="DataMappings" type="string">User_x005F_x0020_Story:|LinkUrl:|Description:|OpenInNewWindow:|Product_x005F_x0020_Name:|Areabranch:|ImageUrl:|Title:{fa564e0f-0c70-4ab9-b863-0177e6ddd247},Title,Text;|LinkToolTip:|ProdcutDesignDocCategory:|Status:|SipAddress:|</property>
        <property name="ListUrl" type="string" null="true" />
        <property name="ShowUntargetedItems" type="bool">False</property>
        <property name="AllowMinimize" type="bool">True</property>
        <property name="GroupBy" type="string">{5c67db99-375a-4afa-a1b0-16f2aac40bb8}</property>
        <property name="FilterIncludeChildren1" type="bool">False</property>
        <property name="BaseType" type="string" />
        <property name="MainXslLink" type="string" />
        <property name="AsyncRefresh" type="bool">False</property>
        <property name="FilterValue1" type="string">HCM/Payroll</property>
        <property name="FilterValue2" type="string">5.7.2</property>
        <property name="InitialAsyncDataFetch" type="bool">False</property>
        <property name="AutoRefreshInterval" type="int">60</property>
        <property name="Filter3IsCustomValue" type="bool">False</property>
        <property name="GroupStyle" type="string">Band</property>
        <property name="AllowZoneChange" type="bool">True</property>
        <property name="FilterIncludeChildren3" type="bool">False</property>
        <property name="EnableOriginalValue" type="bool">False</property>
        <property name="ItemLimit" type="int">3</property>
        <property name="FilterType1" type="string">Text</property>
        <property name="UseCopyUtil" type="bool">True</property>
        <property name="FilterType3" type="string" />
        <property name="FilterType2" type="string">Text</property>
        <property name="FilterOperator2" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterFieldQueryOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Eq</property>
        <property name="PageType" type="Microsoft.SharePoint.PAGETYPE, Microsoft.SharePoint, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">PAGE_NORMALVIEW</property>
        <property name="FilterByAudience" type="bool">False</property>
        <property name="ItemXslLink" type="string" />
        <property name="Hidden" type="bool">False</property>
        <property name="WebUrl" type="string" />
        <property name="HeaderXslLink" type="string" />
        <property name="CacheXslStorage" type="bool">True</property>
        <property name="ListsOverride" type="string" />
        <property name="SortByDirection" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+SortDirection, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">Asc</property>
        <property name="Filter2IsCustomValue" type="bool">False</property>
        <property name="AllowEdit" type="bool">True</property>
        <property name="FeedTitle" type="string" />
        <property name="FilterField3" type="string" />
        <property name="MediaPlayerStyleSource" type="string" null="true" />
        <property name="DisplayColumns" type="int">2</property>
        <property name="Filter2ChainingOperator" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+FilterChainingOperator, Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral,
PublicKeyToken=71e9bce111e9429c">Or</property>
        <property name="XmlDefinition" type="string" />
        <property name="WebsOverride" type="string" />
        <property name="AllowClose" type="bool">True</property>
        <property name="ContentTypeName" type="string" />
        <property name="ListId" type="System.Guid, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089">00000000-0000-0000-0000-000000000000</property>
        <property name="ExportMode" type="exportmode">All</property>
        <property name="NoDefaultStyle" type="string" null="true" />
        <property name="ViewFieldsOverride" type="string" />
        <property name="CatalogIconImageUrl" type="string" />
        <property name="ListDisplayName" type="string" null="true" />
        <property name="Width" type="string" />
      </properties>
    </data>
  </webPart>
</webParts>
<label for="ctl00_MSOTlPn_EditorZone_Edit0g_789619b5_3406_469e_8b24_fc42ff130ea0_CBQToolPartshowItemsFromListRadioButton"></label>
<label for="ctl00_MSOTlPn_EditorZone_Edit0g_789619b5_3406_469e_8b24_fc42ff130ea0_CBQToolPartshowItemsFromListRadioButton"></label>

Hi, 
may i know how many items that you have that CQWP filter for?
because as i remember there should be a limitation on the items number.
http://technet.microsoft.com/en-us/library/cc262813(v=office.14).aspx
http://office.microsoft.com/en-us/sharepoint-foundation-help/manage-lists-and-libraries-with-many-items-HA010377496.aspx
you can try to upsize the threshold but it will affect your environment's performance.
http://blogs.msdn.com/b/dinaayoub/archive/2010/04/22/sharepoint-2010-how-to-change-the-list-view-threshold.aspx
Regards,
Aries
Microsoft Online Community Support
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