I discovered the answer shortly after posting this, but for anyone that stumbles upon this, the issue was in how I was loading the map. I needed to change:
var tileLayer:TiledTileLayer = cast layer;
var tilemap:FlxTilemap = new FlxTilemap();
tilemap.loadMapFromArray(tileLayer.tileArray, width, height, ...);
to
var tileLayer:TiledTileLayer = cast layer;
var tilemap:FlxTilemap = new FlxTilemap();
tilemap.loadMapFromArray(tileLayer.tileArray, tileLayer.width, tileLayer.height, ...);
The original version was using width from the TiledMap, which is the full map width. The second version uses this layer's width. Simple fix!
