I have noticed something in different project directories. There's a little wrench on the icon, but only for certain directories. As an example, the "Source" directory has what looks like a wrench, but the others do not.
This means there are build options set for that folder that differ from the main project.
Thanks Mark, I think I figured out that it may be sensing that some of these directories have different properties as these directories are shared resources being used by mutliple projects. Don't know if that's also creating the Git issue I've been trying to figure out, but it seems the Git issue is not consistent.