Ajax ignoring my default_value
Alright, so this is slightly hackey, but I got this to work. I totally gave up on trying to set a default value in the render array, and instead did the drupal_render and set it to a variable. I then modified the html directly in the variable. The code I originally posted now looks like this:

if(isset($id) &amp;&amp; is_numeric($id)) {
  $newrender = drupal_render($newdata);
  $newrender = str_replace('value="'.$id.'"', 'value="'.$id.'"  selected="selected"', $newrender);
}

$commands = array();
$commands[] = ctools_modal_command_dismiss();
$commands[] = ajax_command_html('#measure-data-source', $newrender);
print ajax_render($commands);
exit();


If anyone on here has a more elegant solution, I'd be happy to know the "correct way" of doing this, but this produces the desired result.