Override Another module's Template file using my Custom Module (Drupal 7)
I had to use the following snippet to get it to work. I think it may be due to the way I set up the original template.

&lt;?php
//  unset the original template to set yours.

// Implement hook_theme_registry_alter
function MODULENAME_theme_registry_alter(&amp;$theme_registry) {
  $theme_registry['TEMPLATE_TO_OVERRIDE']['template'] = drupal_get_path('module', 'MODULENAME') . '/TEMPLATE_TO_OVERRIDE';
  $theme_registry['TEMPLATE_TO_OVERRIDE']['theme path'] = drupal_get_path('module', 'MODULENAME');

}