The "Nintex Workflow Scheduler" timer job is tasked with starting any Nintex Workflows that have been scheduled in the SharePoint farm - this job executes within the SharePoint timer service (OWSTIMER.exe). In addition to this coupling to the SharePoint timer service, some Nintex actions, primarily the delay based actions, are executed within the SharePoint timer service when they are rehydrated into memory after idling in an inactive state.
The Nintex Workflow Scheduler job should only have one instance listed in the Timer Job Definitions page. To check, please go to Central Administration > Monitoring > Timer Jobs > Review job definitions. Scroll through until you locate Nintex Workflow Scheduler. There should be only one instance there. If there are more, all but one will need to be deleted, ensuring the one that is left is on a web application on a server running the “Microsoft SharePoint Foundation Web Application” service.
When the product is installed, by default, the Nintex Workflow Scheduler will be placed on the server hosting Central Administration. This will be changed in the future, as the web application which represents Central Administration does not always have the Microsoft SharePoint Foundation Web Application service on it.
To check, go to Central Administration > System settings > Manage servers in this farm. The Microsoft SharePoint Foundation Web Application service is generally considered to be a web front end service.
To change this, the NWAdmin.exe InstallTimerJob and UninstallTimerJob operations can be used to bind the timer job to a Web application running the Microsoft SharePoint Foundation Web Application service. Doing this will ensure SharePoint executes scheduled workflows on a web front end servers, so any content web application running the web application service will do (only one per farm).
The nwadmin.exe command line tool is used. Full information here NWAdmin Operations - Nintex Workflow 2010
Please type (do not copy and paste) these commands:
1. NWAdmin.exe -o UninstallTimerJob -job ScheduledWorkflows
(Use above line if it is currently installed on Central Admin Web App, if not specify what Web App to remove it from using -url switch)
2. NWAdmin.exe -o InstallTimerJob -job ScheduledWorkflows -url http://yourwebappurl/
Naturally, you will need to replace http://yourwebappurl/ with the real URL of the relevant web application you choose to install it on.
NOTE: Only scheduled workflows use the Nintex Workflow Scheduler service. Any regular workflow is run at first by the "w3wp.exe" service and once having been "put to sleep", then after by "owstimer.exe", the SharePoint Timer service. Moving the Nintex Workflow Scheduler will not interfere with regular workflows at all.
Install, Uninstall and reinstall can be done during business hours, there is no resets, down-time or any impact to workflows. The timer job will pickup where it left off after reinstall and run any schedules that were missed during reinstall.
If using SP2013, click the gear icon in the upper right corner, then click Nintex Workflow 2013, then click Schedule Site Workflows.
There you can setup a schedule for your site workflow.