I'm guessing a bit here, since I don't know the Mapbox JS very well, but it sounds a lot like an async error. Strangely, I don't see anything in the Mapbox or Leaflet APIs about a callback for this function. But, you can pass straight GeoJSON to featureLayer(), so I'd suggest using jQuery (or your XHR library of choice) to grab the data:
var map = L.mapbox.map('map', '<MapBoxID>');
var zipLayer;
$.getJSON('data/blah.json', function(data) {
zipLayer = L.mapbox.featureLayer(data);
zipLayer.addTo(map);
zipLayer.setStyle({color: 'red'});
});
Hopefully that'll do the trick.