In our installation (SP 2013, Nintex 2013) we realized that some lists/libraries had no options to create an manage Nintex workflows. The options had been missing in the workflow settings menue.
As I found other unansered tasks in the internet I'd like to share our solution.
The errorous lists had been created by a list template. The template used the content type "element" with a different content type ID than "element" on the SharePoint server. By allowing content type management in the list, the current unknown content type can be renamed and the standard content type can be added to the list. This leeds to the appearence of create / manage Nintex workflow links in the wirkflow settings section but not to the Nintex specific entries in the item context menu like "View Workflow History" and "Sheduled Workflows"; to get these entries, the content type of each item has to be changed to mach the one with the system-known ID.
Go to list settings -> advance settings -> allow managing content types.
Go to list settings -> click on content type -> change name (as it's not able to use two types with the same name)
Go to list settings -> add content type -> add content type
Go to list settings -> click on (to be deleted) content type-> delete content type
Go to list settings -> advance settings -> disallow managing content types.
Hope this helps some of you.
Best regards Michael