The urls that ngx_pagespeed can generate are bounded by a setting called 'MaxSegmentLength' [1]. There are good reasons for that. This implies that the amount of files that can be combined into a single url is bounded as well. That might be what is causing the 14 css files to be combined into 3 urls, instead of 1.
Skipping minification of javascript can be because of these things: - The javascript was diagnosed to be introspective [2]. - The javascript contains parse errors.
It might be worth having a look at nginx's error.log, and check the configuration loading messages and the output of ngx_pagespeed on the first request in there, to figure out what is wrong.
[1] See "Limiting the maximum generated URL segment length" at https://developers.google.com/speed/pagespeed/module/restricting_urls [2] See "Restricting PageSpeed from rewriting URLs of introspective JavaScript" at the url above.