Found your zipped project, extracted it (Ignored the __MACOSX thingie) and opened it. with KiCad’s project manager.
(I just started this reply to post the screenshot. I will do multiple edits and commits as I go along. So try to be a bit patient).
First weird thing when opening the schematic is:
Schematic looks like a normal schematic.
PCB looks like your screenshot.
Pcbnew / File / Board Setup / Design Rules / Net Classes looks like it should on my system: I see all the nets in the Net box:
Then I go back to the schematic, and update the board with [F8]. It complains about missing footprints for switches.
All the red texts in:
I do not know what your intention is with these components, but if the components are not on the PCB, then they also are not in the netlist.
On your schematic I see that some components are placed off-grid.
It is very strongly advised to always place components on a “50” (or multiple thereof) grid. It’s a sort of long standing and known KiCad bug that component pins endpoints have to lineup with the green line ends and there is no snap (yet). Keeping all components on a “50” grid is an easy workaround all beginners have to learn untill there is a real “snap” function in Eeschema. In your particular case the connections do seem to be reflected in the netlist, so it’s not the problem you try to adres here.
In the Net Classes I can see you have assigned 3 nets to “Power”, by selecting that net in the "Net class filter:
Most of the other nets are in the “Signal” net class. So apparently you have managed to change this in the past.
I’ve renamed your project folder, and saved the file in my KiCad V5.1.5 version. Then also removed the “take1.kicad_pcb” and some backup files, and then zipped the whole directory:
Engineers_Thumb_2020-03-21T17:46.zip (229.7 KB)
Does this version behave any differntly on your PC? Can you work with the net classes now? Does anything happen when you click on the buttons on the Board Setup window?
Edit yet again:
I’ve had a little bit closer look at your schematic.
The missing footprints are obviously intentional.
If you put an # in front of the reference field, you tell KiCad to exclude these components from the BOM and the PCB. Like this: