In the GUI when you turn off a section it turns everything off in the section. To enable one layer you have to turn the section back on and you see everything that is enables. So the code above works as designed.
You need a loop that walks through all the items in that sections and turns them off.
Set FRED = pcbDoc.UserLayers
For Each lay In FRED
pcbDoc.ActiveView.DisplayControl.UserLayer(lay.Name) = False
Sometimes you are so focused on a certain solution that you miss the obvious.