Original report (archived issue) by Philip Starkey (Bitbucket: pstarkey, GitHub: philipstarkey).
If you have all groups in a globals file set as active, except for one, and then delete the one that is inactive, the checkbox indicating the "active" status of the whole file stays in the "partial" state rather than updating to "checked".
See image below. Note how the checkbox has a square in it instead of a tick because I just deleted the only inactive group!

Note that this has no material effect, other than to look odd. It corrects itself if you change the active state of any of the remaining groups or restart runmanager.