Setting value to checkboxes in a form
$form: An associative array containing the structure of the form,
  which is passed by reference. Form validation handlers are able to
  alter the form structure (like #process and #after_build callbacks
  during form building) in case of a validation error. If a validation
  handler alters the form structure, it is responsible for validating
  the values of changed form elements in $form_state['values'] to
  prevent form submit handlers from receiving unvalidated values.


So your form validation function should be as the following:

/**
 * validation functoin
 */
function myModule_search_validate( &amp;$form, &amp;$form_state ) {
  // function body
}


Then in your form submit function you need to set $form_state['rebuild'] = TRUE as following:

/**
 * submit functoin
 */
function plant_Ontlogy_search_form_alter_submit( &amp;$form, &amp;$form_state ) {
  // function body

  $form_state['rebuild'] = TRUE;
}


If setting state rebuild to TRUE didn't work with you by itself, try to set default value as the following example to each additional field:

$form['myM_options']['entity'] = array(
  '#type' =&gt; 'radios',
  '#title' =&gt; 'Search by',
  '#default_value' =&gt; isset($form_state['values']['entity'])? $form_state['values']['entity'] : 'gene',
  '#default_value' =&gt; 'gene',
  '#options' =&gt; array(
    "gene" =&gt; "Genes",
    "ortholog" =&gt; "Orthologs",
    "microarray" =&gt; "Microarray Features"
  ),
);