Twins explains it. On a shield, the physical part would hit and be absorbed, thus dealing zero damage. Since it dealt zero damage, the shadow portion of the ability wouldn't even occur.
(Using the door strat isn't the best defense!).
As to the macro issue, that's always happened with dual specs. It's simply a graphical thing; the actual ability will still use the max rank.
The physical part and the shadow part of your Scourge Strike should deal near identical amounts of damage, now that the latter doesn't crit. Technically, the latter should deal slightly more (since it has a, what, 107% or so modifier?), but nothing that significant.
WoW Meters Online - Combatlog Replay from this evening, for example. Almost exactly the same damage from both parts. It's nothing abnormal.