Scheduled site workflows are unexpectedly running twice, or not running at all.
Remove and reinstall the Scheduler job, making sure it is only installed on one Web Front End server:
Go to: Central Administration > Monitoring > Job Definitions
Look for the "Nintex Workflow Scheduler" and delete all instances but one.
There will likely be more than one scheduler listed - there should only be one. Delete any that are not on Web Front End servers.
This is generally caused by a duplication of the Nintex Workflow Scheduler timer job. If this is installed on more than one server in the Farm it will run duplicates of a workflow or often fail to run at all.