Hi all,
We had the same problem but we know what the probem was back then. SharePoint was creating 2600 mysites for all users... because of this unfortunate event:) all other SharePoint/nintex jobs became 'pending'. It uses first in first out:) and there were 2600 mysite jobs before the SharePoint/Nintex job. People could approve there task, but the workflow and remained pending and the workflow was locked.
So what I'm trying to say is that SharePoint sometimes needs to update a field or do something else(check in, check out), but this job only runs every 5 minutes... In some workflows we created a delay step (minimum = 5 minutes), just to make sure that SharePoint did what he needed to do.
Try this and see if it helps:)
Regards,
Jaap