I just deployed Nintex WF to a SharePoint 2013 farm. No errors in installation. I deployed the solution to all Web apps. Used central admin > Nintex WF management to activate on all Web apps.
The only site settings > site collection features that the Nintex WF item appears under is for central admin site collection (portalca.xxx.com:2222).
None of the other web applications/site settings/site collection features shows it. There are several Web apps all on port 80 so portal.xxx.com, portaldev.xxx.com, portalqa.xxx.com.
The CA as indicated is portalca.xxx.com:2222.
I just logged a support case but the community might have seen this sort of problem before too.