The nginx.conf file automagically created by W3TC (default location, root web directory) only contains the W3TC Browser Cache settings, and omits Page Cache cache, Page Cache core.
On the w3tc_install page it shows all the proper Cacheing settings (and their appropriate nginx.conf directives) -- yet when W3TC creates the nginx.conf file it does not reflect the additional directives beyond Browser Cache.
My workaround has been to copy the directives listed in the W3TC Install tab to my /sites-available/sitename nginx conf file, but id prefer to use the method described in the inital setup to allow for changes to W3TC via the WP Dashboard.
Ive deleted nginx.conf file generated by W3TC, and confirmed permissions and timestamp -- W3TC has access to read/write that file, and recreates it after deletion, but as mentioned above its omitting all settings beyond Browser Cache.
My setup: EC2 | Ubuntu 12.04 | nginx 1.1.19 | WordPress 3.3.2 | W3TC 0.9.2.4