My Kelin Kelilin game is using Tiled as well. The method I use is different but it can show layer as many as I want. My method uses tmx file as from Tiled, since the file itself is already an XML.
public function addTiledLayer(LayerName:String, TilesetPath:String):Void
var flxtilemap:FlxTilemap = new FlxTilemap();
tiledTileLayer = cast(_map.getLayer(LayerName), TiledTileLayer);
flxtilemap.loadMapFromCSV(tiledTileLayer.csvData, TilesetPath, tmxTiledMap.tileWidth, tmxTiledMap.tileHeight, null, 1);
@IBwWG hmm, that's strange. I'm not noticing any difference when going back and forth between fullscreen/windowed (I'm base 1920x1080 downscaled to 1280x720 windowed, then 1920x1200 on fullscreen since I'm on a 16:10 monitor)