I see the similar problem when I try to use first param_value as a filter on the second input selection and then second on the third input selection. The code works fine and makes right selections but displays the warning message “An invalid option was selected, please verify”. 

My select code is similar: 

<param name="inputmodel" type="select" size="100" label="Input Model" area="True">
       <options from_file="coyote.loc">
            <column name="name" index="2"/>
            <column name="value" index="2"/>
            <filter type="unique_value" column="2"/>
       </options>
      </param>
      <param name="inputSize" type="select" label="Box Size" selected="false">
       <options from_file="coyote.loc">
            <column name="name" index="3"/>
            <column name="value" index="3"/>
            <filter type="param_value" ref="inputmodel" column="2"/>
            <filter type="unique_value" column="3"/>
       </options>
      </param>
       <param name="inputRealization" type="select" label="Realization based on different seed values" selected="false">
           <options from_file="coyote.loc">
            <column name="name" index="4"/>
            <column name="value" index="4"/>
            <filter type="param_value" ref="inputmodel" column="2"/>
            <filter type="param_value" ref="inputSize" column="3"/>
            <filter type="unique_value" column="4"/>
       </options>
       </param>
      <param name="input" type="select" size="300" label="Input Snapshot" area="True" help="Choosing Input Snapshot files" selected="false">
        <options from_file="coyote.loc">
            <column name="name" index="6"/>
            <column name="value" index="6"/>
             <filter type="param_value" ref="inputmodel" column="2”/>
             <filter type="param_value" ref="inputSize" column=“3"/>
             <filter type="param_value" ref="inputRealization" column="4"/>
          </options>
      </param>

Did you figure out where the problem is? 

Thanks,
Saba