What would be on your checklist when trying to debug a non-reverting feature?
Do you have any modules implementing hook_strongarm_alter()?

If you're blindly overriding Drupal system variables using hook_strongarm_alter() as follows:

function mysite_strongarm_alter(&amp;$items) {
  $items['upload_extensions_default']-&gt;value .= ' qtz';
}


...some Features may incorrectly appear as Overridden.

Instead check to see whether the item is defined first:

function mysite_strongarm_alter(&amp;$items) {
  if($items['upload_extensions_default']) {
    $items['upload_extensions_default']-&gt;value .= ' qtz';
  }
}


...and the Strongarm aspect of the Feature will no longer incorrectly appear as Overridden.