I see that the alignment is fixed, I would know what is your sort issue just by looking at the gallery but I ran a few test and custom, title and time sort work fine.
For your settings. all galleries have gallery specific settings that overwrite the global settings. you can change the settings but you will have to check each gallery.
To allow the images to open using the lightbox, uncheck “Link image to attachment ” to get the pagination back just add a image limit on settings > gallery > image per page