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After some debugging I've discovered that the "translate and reference" feature (which is fantastic) doesn't work on syncronized fields.
The _noderelationships_nodeapi_prepare_translation() works fine: it correctly set up the translate_and_reference[] array on the $node variable, but after doing that, the i18nsync module rewrites the value.
I'm not sure if this is a noderelationships bug or an i18nsync one... I've temporary wrote a small fix for the i18nsync module ( http://drupal.org/node/1300404 ) but I'm not sure if it is the right way to do.