After testing the source of your website (that you sent me in private) I found what is causing problems with the Pagination.
In line 67 of your config.toml you have the following parameter:
home = [ "RSS", "HTML"]
The order of Output Formats matters.
Reverse what you have and then the .Paginator next and prev navigation links will output HTML.
i.e. home = [ "HTML", "RSS" ]
Incidentally this the second time today that I am seeing this setup.
Can you please tell me where did you get the idea about entering the RSS Output Format first?