Now I may be wrong about this and will be working on testing it in game in the near future but I think protection from Alignment's duration is much shorter than it is actually supposed to be. The spell should be lasting 5 minutes per level but it seems to be lasting something much shorter than that, I would wager minutes per level. It seems to expire much more quickly than other buffs of its duration, and has become very unreliable as a source of AC and extra saving throws in fights unless you're using it right then and there from an item as a result.
I will do further testing to verify this.