Hi Jim,
Since you're on version 5.2 I can't speak to much about it since I was not with the team at that point.
What I can tell you is that since the version 5.3 release I dealt with one case somehow related with your issue.
That was about a SharePoint migration (2007 to 2010) that involved a lots of SP out of the box workflow and Nintex workflow migration and the customer experienced an issue with Nintex worflows.
To troubleshoot that I provided him some custom code that triggered a workflow with debug information. It looked that he figured out the solution since he hasn't got back to me.
The issue that you mention from 5.4.1 release notes has been fixed.
PS
I can provide the same custom code to you if you think that could help (hope that it works with QWP 5.2).