Firstly, in your template you really should have at the very least, PostLoop. That should be in every Content Area template except the 404 Error template.
You may have boxes added and cloned in Page Templates, Header or other templates we're not seeing. The other things showing up in your PageLines Meta Settings are likely in other parts of the site via Drag & Drop. For example, you show the Content Area for Template 1, but you have Primary Sidebar in the settings, which means it's going to likely be located in SB1.
If you give a good and thorough look around to all the possible options in Drag & Drop, you're likely going to find everything. Rest assured, sections don't mysteriously appear in the PageLines Meta Settings if they're not in the templates, somewhere.
Also, in Page Templates, make sure Content is present for all the templates except the 404 Error one.