I was "messing" with the display properties of a list and when I went to do some work on a workflow I found the Nintex Workflow controls were gone! I found they were still available on other lists/libraries on the site. I still tried removing and readding them in the site features, but still missing.
A quick search turned up this entry on Nintex Connect. I had modifed the toolbar on the list... so I clicked Site Actions --> Edit Page and changed the list webpart properties back to Full Toolbar. That restored Create a Workflow and Manage Workflows with Nintex Workflow.