Bug submitted via the Visual Studio Marketplace.
When the "Pending Changes" pane is used undocked from the "Team Explorer" pane (using the diagonal arrow in the top right corner), then, sometimes, when Visual Studio is restarted, the buttons All Files/Included/Excluded seem to stay always disabled.
A workaround I found is to close the "Pending Changes" pane to dock it back into the "Team Explorer" pane, and then undock it again.
Not sure if we'll be able to fix this, as it may just be a bug with Visual Studio notifications, but we can take a look. Maybe there's an additional event notification we can watch for.