Markers created with circleMarker behave oddly before and after RaphaelLayer Features are used.
It can be reproduced inside the demo by placing this little script into the index.js file:
(function() {
var map = new L.Map('map');
var tiles = new L.TileLayer('http://tile.openstreetmap.org/{z}/{x}/{y}.png', {
attribution: '',
maxZoom: 18
});
L.circleMarker([-34.810835031000003, 138.516159968000011],
{radius: 10,
color: '#0f0',
opacity: 1,
weight: 2,
fillColor: '#0f0',
fillOpacity: 0.5}).addTo(map);
var adelaide = new L.LatLng(-34.93027490891421, 138.603875041008);
map.setView(adelaide, 10).addLayer(tiles);
// comment this out and the circleMarker will be visible again
var m = new R.Marker(adelaide);
map.addLayer(m);
})();