When ContentByQueryWebPart.ViewFieldsOverride property is specified, it overrides default list field names used to filter the set of list items. It means all the required fields have to be specified explicitly, in your case it would be:
<property name="ViewFieldsOverride" type="string"><![CDATA[<FieldRef ID="{fa564e0f-0c70-4ab9-b863-0177e6ddd247}" Nullable="True" Type="Text" /><FieldRef ID="{94f89715-e097-4e8b-ba79-ea02aa8b7adb}" Nullable="True" Type="Lookup" /><ProjectProperty Name="Title" />]]></property>
where Field IDs
fa564e0f-0c70-4ab9-b863-0177e6ddd247: Title
94f89715-e097-4e8b-ba79-ea02aa8b7adb: FileRef
Manifest example: aggregating Discussion items
<webParts>
<webPart xmlns="http://schemas.microsoft.com/WebPart/v3">
<metaData>
<type name="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart, Microsoft.SharePoint.Publishing, Version=14.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<importErrorMessage>Cannot import this Web Part.</importErrorMessage>
</metaData>
<data>
<properties>
<property name="Title" type="string">Discussions</property>
<property name="SortByDirection" type="Microsoft.SharePoint.Publishing.WebControls.ContentByQueryWebPart+SortDirection, Microsoft.SharePoint.Publishing, Version=14.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">Desc</property>
<property name="ContentTypeBeginsWithId" type="string">0x012002</property>
<property name="SortBy" type="string">{28cf69c5-fa48-462a-b5cd-27b6f9d2bd5f}</property>
<property name="WebUrl" type="string"></property>
<property name="ServerTemplate" type="string">108</property>
<property name="DataMappingViewFields" type="string">{b9e6f3ae-5632-4b13-b636-9d1a2bd67120},Computed;{543bc2cf-1f30-488e-8f25-6fe3b689d9ac},Image;{fa564e0f-0c70-4ab9-b863-0177e6ddd247},Text;</property>
<property name="ViewFieldsOverride" type="string"><![CDATA[<FieldRef ID="{fa564e0f-0c70-4ab9-b863-0177e6ddd247}" Nullable="True" Type="Text" /><FieldRef ID="{94f89715-e097-4e8b-ba79-ea02aa8b7adb}" Nullable="True" Type="Lookup" /><ProjectProperty Name="Title" />]]></property>
</properties>
</data>
</webPart>
</webParts>