Currently when you call addLayer while the MarkerClusterGroup is on the map it will add/remove/update markers on the map as it goes.
Need to investigate if this is a performance issue, if it is then add some new methods:

bulkAddBegin: Stops addLayer from adding/updating/removing layers on the map
bulkAddEnd: Adds all layers that should be on the map to the map.

This is for the cases where you load 1000s more markers via AJAX later.