Hello dlewis,
The "Warning 39" is a OS bug that has been changed into a warning so it is possible to compile the project.
This Error are in certain HWDs and they are working on a solution.
We have found a workaround to "remove" it, buy moving the "Inputs" block before the "Unit_Config block". Then the error should go away. (In the image is a SC050, that's what I had open in GUIDE).
Have a nice day.