I found out why nothing is being displayed when there is no layers in the base room. The layers being created from room_pack_load have depths that are higher then the background layer. Because of the this the background is being drawn above it. I'm not sure why having 2 tilemaps already being created in the base room fixes this issue but maybe it pushes the background layer higher up? Still not sure on why I can't correctly read the layers though. My work around for that though is to store the tilemaps using room_pack_store_tilemaps and then reference those instead.