Ther is an article by Aaron Labiosa on how to resolve an issue where workflows no longer show up in the workflow gallery. You can see the article here
In this article he is speaking about a site that has been migrated and so the SharePoint list ID is no longer valid. Step 4a is a bit cryptic since it assumes the field is editable, which on my site it is not even though the edit form shows the field being available. Maybe it only actually displays if the field has a value to eidit in the first place?
Here's my situation. This is happening on a brand new 2013 site. We recently upgraded our Nintex Workflow engine from 22.214.171.124 to 126.96.36.199 and thats when it started happening. It happens randomly which makes it more maddening. Specifically workflows are not showing up on _layouts/15/NintexWorkflow/WorkflowGallery.aspx. In his article he says to navigate to /NintexWorkflows/Forms/AllItems.aspx and update the list association id there. I checked that location on a site which is displaying workflows correctly and there is no list association ID in that library either so it appears that is not relevant to the situation.
Here is the screenshot of the list that is not always getting populated with published workflows just to be clear:
This is the library you get to by choosing 'Manage Workflow Inventory'.
Any ideas why this might be happening?