I started having this exact issue recently as well. If my 3D Scene has more than say 4-5 layers it does not load properly in the 3D Web App.
More specifically, if it is a new browser session, it will usually load the first time with all the layers showing. Then on refresh, it will move the top layer to the bottom and name it "untitled layer" as you state. In addition there is no way to turn off the layer. If I open a new browser session or go "incognito" in chrome, the issue will go away until I reload the page again. So it appears related to the browser cache.
Looking for some input on how or why this is happening.
For the time being I have to put a "blank" layer at the top so that all the layers I want to interact with are still present when it changes to untitled layer.