Make sure you're copying field names exactly as shown in REST. For example, this map: http://maps.tnc.org/coredata has the following xml to support a joined table: <layer>
<definitionexpression></definitionexpression>
<enableexport>true</enableexport>
<name>Conservation Projects</name>
<url>http://maps.tnc.org/ecadpubprodanon/rest/services/conservation_projects_anon_WM/MapServer/1</url>
<!-- expression is for the "text search" function; users will enter [value] and you determine how that input is used to return records -->
<expressions>
<expression alias="Search by Name" textsearchlabel="Find Conservation Projects by Name:" usedomain="false" field="CP_STEWARD.PROJECTS.PROJECT_NAME">lower(CP_STEWARD.PROJECTS.PROJECT_NAME) LIKE lower('%[value]%')</expression>
<expression alias="Search by ID" textsearchlabel="Find Conservation Projects by ID:" usedomain="false" field="CP_STEWARD.PROJECTS.PROJECT_ID">CP_STEWARD.Project_Polys.PROJECT_ID=[value]</expression>
</expressions>
<graphicalsearchlabel>Find details about conservation projects by clicking on one of the tools below, then clicking on the site you want to find out more about (read the help for details).</graphicalsearchlabel>
<spatialsearchlayer>false</spatialsearchlayer>
<titlefield>CP_STEWARD.PROJECTS.PROJECT_NAME</titlefield>
<!-- Rather than specifying each field, you can simply return all fields by changing "false" to "true" below and deleting or commenting out the field name tags -->
<fields all="false">
<!-- The field tag must include the actual field name, but can optionally include "alias" or "dateformat" or "gridfieldonly" or many more. Note that if you don't manually specify an alias the alias from your mxd will be used (or the field name if no alias exists) -->
<field name="CP_STEWARD.PROJECTS.PROJECT_NAME" gridfield="true"/>
<field name="CP_STEWARD.PROJECTS.PROJECTORG" gridfield="true"/>
<field name="CP_STEWARD.PROJECTS.CONTACTORG" gridfield="true"/>
<field name="CP_STEWARD.PROJECTS.CONPRO_URL" hyperlinkgridfield="true" hyperlinkaliastext="Open ConPro record" alias="ConPro URL"/>
</fields>
<!-- If the link has an extension of .jpg, .gif, or .png a preview image will be displayed, otherwise a clickable "i" symbol will show up for the link -->
<linkfield>CP_STEWARD.PROJECTS.CONPRO_URL</linkfield>
<icon isfield="false"></icon>
<zoomscale usegeometry="true"/>
<autoopendatagrid>false</autoopendatagrid>
</layer>