The last Zenphoto 1.4.13 master and this version changed my RewriteBase from "/" to "//". So, I changed it back. Also, makes the .htaccess file read only on Windows and 444 on Webhost so I undo that as well.

I wonder if it gets confused in thinking it's installed into a subfolder, and that it's a new install?

Thanks. Apparently a previous change doesn't work as it should.
I opened an issue on GitHub but it will take some time before @acrylian can look into it due to personal circumstances.