I'm not sure if this would help, but I had a similar problem when I was writing an script that included freezing certain stacks to preserve certain deformers.
Render Region just stopped working every time I ran the script, but after a SI restart everything was back to normal. I just dropped the freezing function and it worked as it should. At the end I really didn't need the freeze function and I didn't have time to dig into it so I'm not sure where exactly was the problem. Maybe some of your tools can be doing something wrong? M.Yara
