After creating a new workflow status and associating it to "Done" column of an Agile Board, JIRA will show its transition on the mentioned column.

Steps to reproduce:
1 - Select a workflow with 3 statuses: Open, In Progress and Resolved.
2 - Add a new status with "To Do" category.
3 - Create back and forth transitions (cardinality 1:1) between the new status and Open status.
4 - Create back and forth transitions (cardinality 1:1) between the new status and In progress status.
5 - Create a Project with any simple issue tracking and associate it with the workflow created before.
6 - Create a Scrum board from an existing project and associate it with the project recently created.
7 - On Board > Configure Board > Columns drag the Unmapped status (the one created previously on step 2) to the "Done" Column.
8 - Create some issues and Start a Sprint. Move the issues from "To Do" to "Done" column. You'll see the transition related to the status recently created on mentioned column.

JIRA Agile v7.0.0-D20150819T011040