Ashley I know it's an old and closed report, but can you please update the Layer manual page to let users know that the "Initial visibility" don't reset after the layout restart? It shouldn't take more than a minute. It would be fine if you only publish the update with the next stable release.
I just found myself in that situation where I didn't know how my project does what it does and I couldn't find any actions related to setting the layer visibility. I searched the manual and I found this topic. This is the second time as I recall, because when I first started the project I had this issue as well. Logic dictates that the layer will set it's visibility each layout start based on it's setting in the editor, just like objects do.