Bale
Minion
I don't see anything which looks like a likely culprit, even though I know the purpose of many of those preferences.
The later. Only preferences which are manually set or have a default value will show up in your preferences file. masterRelayOverride doesn't have any default value, not even a blank one. Since preferences without a value are treated as if blank when queried, that works.
Another note, I failed to find masterRelayOverride in Global_prefs.txt and in mellissaleo_prefs.txt. Is it supposed to be stored somewhere else? Or it doesn't show it it doesn't have a value?
The later. Only preferences which are manually set or have a default value will show up in your preferences file. masterRelayOverride doesn't have any default value, not even a blank one. Since preferences without a value are treated as if blank when queried, that works.