Another variation on adding the Pause would be to set it to 1 minute instead of 5. Another would be to try the "Commit Pending Changes" action instead of the pause. Haven't tested this one in your situation though.
The default timer job resolution in Sharepoint (the "clock tick" of the workflow engine) is 5 minutes, so setting the pause to 1 min is not always going to give you quicker result.
Whan I tried this it errored-out just like Alan's experience. I can't remember if the workflow contained a Set Item Permissions action which seems to be the probem in his case.
This would be an awful lot easier if Nintex just gave us a "start with no start form" workflow property.
I use this technique, and with Nintex forms you can add a button to the form, and link the button to the Flag field and have it set the value to Yes.
Just make sure you also add another step to your workflow to set it to "-" at the beginning so that it does not run the next time someone presses save.