Okay, so I've been using Construct 3 since it was released and it never saved my layout. Never did I think it was an issue on my end. Checked on a different browser and it works...
Reset my cookies and it's saving now. It must have been a corrupted cookie or something. Jeez. Thanks!
I'm putting this warning on both my posts in case someone is still using that type of backup, which you shouldn't by the way.