This one has got me believing that this is a bug with the Mixer Scenes and not something that is there by design.
When switching between Scenes i have both the Track List and Console List open (both display the Mixer Scenes view) but what is concerning is that when switching the Console view will show that i have select a different Mixer Scene but the Track List view still has the previous Scene selected. Now when i make any changes to the faders and hit Update Scene it updates the previous scene and not the current one, basically undoing all the hard work i've done previously.
The picture above shows Scene 2 selected in the Track List but look closely and you'll see in the Console that Scene 1 highlighted.