The relevant scripting code is
Regions.Source_Unselected.Check(mapWindow);
This line is the same code for all of my regions. Only the region name changes.
I'll attach the screenshots you requested. Please let me know if I can help in any other way.
Is it possible that the method of region checkpoint creation makes a difference? For example, some of them were created while recording a test. Others were created manually and then referenced from a test script. All have at least once after they were created. I will try different ways of creating them and see if that has any effect.