I run nightlies, but not the latest latest, mine are 2 weeks old I think.. so I don't know if stuff has changed.
Anyhow, the way to set up the footprint libraries is either through CvPCB or PCBnew.
Personally I don't use CvPCB, as my personal libs contain the links to the footprints already.
Thus I go via PCBnew if I want to change anything on the setup of the footprint libraries.
I also don't use the Wizard.
If you installed the latest and the fp-lib-table (with the links to the footprint repos) hasn't been updated with the latest stuff that's been going on in the KiCAD-github repo then they;re out of sync.
To get them back in sync the way I would try would be to start up the wizard and let it find all those footprint libs in the repo and add them to my install - if I needed them.
That's why I posted above screenshot of this..
PCBnew>Preferences>FootprintLibrariesWizard (right on top)
CvPCB is a tool that helps you link components (schematic symbols) to footprints. Nothing more, nothing less.
It doesn't matter which of the functions/tools of KiCAD you start when and how. It's KiCAD.
The Footprint Library Manager is reachable via CvPCB,
but the Wizard is not (at least not in the nightly I got installed) - thus, but I gave you the short and easy way out (I hope that it works that way - you just point the wizard at the repo and it does the rest). That's why it has been implemented afaik, to make this kind of thing easier.
If you want to do it the 'hard' way.. open the Lib Manager via CvPCB and do it yourself - library by library.
First delete the entries that can't be found and then add the ones you think you're missing.
No idea if that is more fun.
As a final option I can offer this - find the fp-lib-table in your KiCAD program settings folder and edit it with notepad - did that myself a couple times, but not in regards to the github stuff.