Field templates not recognized in sub-theme

No. This project doesn't touch fields in anyway. I know for a fact they work though because in several projects I do, I use field overrides quite frequently. The only thing I can think of (off the top of my head) is that you're not actually using the correct field name. The easiest way to figure this out is to do a preprocess on all fields and detect the field name via:

/**
 * Implements hook_preprocess_field().
 */
function YOURTHEME_preprocess_field(&$variables) {
  $element = $variables['element'];
  // If you have devel enabled, otherwise:
  // var_dump($element['#field_name']);
  dpm($element['#field_name']);

  // You may also want to check the existing suggestions:
  dpm($variables['theme_hook_suggestions']);
}

There is a possibility that #2098551: Registry alter does not keep proper order of [pre]process functions is related, but I highly doubt it since this is regarding a template. It could be related to #2228943: [REGRESSION] Template suggestions not being used though. Definitely need more information before we can proceed further.

Ah, yeah... that module :) FWIW, Display Suite has the ability to override field templates in their ds_extras sub-module. It works, much better IMO, as you can explicitly select the fields you want to override.