Issue
A workflow with a pause action takes a long time to complete.
Resolution
The pause action is dependent on the healthy functioning of the Sharepoint Timer service.
When the sharepoint timer service is overwhelmed by several other timer jobs, this has a cascading effect on any workflow actions that are dependent on the Sharepoint Timer service.
To confirm if the Sharepoint Timer service is impacted by other timer jobs, please create a new Sharepoint Designer workflow and a new Nintex Workflow, and add a pause/delay action with a 1 minute pause.
Then start the workflow and observe if it completes after 1>6 minutes, if both workflows take longer than this or do not complete, then it would indicate a problem with the Sharepoint Timer service.
Which would then require further investigation as to what Sharepoint timer Job is draining additional resources or if it is possible to enable the Sharepoint Timer service and Sharepoint Workflow Timer service on any other members with the farm.
Additional Information
It would also be advisable to check the size of the Workflow History List and Workflow Progress table, as these could also affect the performance of Nintex workflows.
Please refer to this blog on how to check the size of both history list and the workflow progress table: https://community.nintex.com/community/build-your-own/blog/2014/10/07/demystifying-workflow-history-part-1
You can purge the history list and the progress table by referring to this blog:
https://community.nintex.com/community/build-your-own/blog/2015/09/16/how-to-purge-large-history-list-and-dboworkflowprogress-table