GMRoomPack tries to find room's each layer by name (via layer_get_id), and, if there isn't one, creates it at the original depth.
Needless to say, this makes issue #2 a bit mysterious - perhaps you are loading a room with another controller object and GM declines to create duplicate layers? I'd suggest to try logging IDs of your grid layers.
As of issue #1, are you loading multiple tilesets into the same room? You might need to store the actual tilesets into a separate list (and loop over them) but it's hard to tell with this little context.