Hey, I'm one of the people from Ask Mr. Robot. I wanted to drop by and let you know of a few things.
1) We've been working with Theck to make sure we have the best Paladin stat weights that we can. We just got some updated weights from him and will have these incorporated this week
So you might see a few optimizations change once we do that.
2) Mr. Robot accounts for all racials, socket bonuses, enchants, profession bonuses, raid buffs, etc. So when you try to reach caps, Mr. Robot already knows what you have and factors that in when optimizing.
3) Mr. Robot looks at every combination of gem/enchant/reforge. This allows him to optimize the whole picture.
I have some more information on how Mr. Robot's optimizer works, for those interested:
http://blog.askmrrobot.com/2012/10/h...ptimizer-work/
Silverhatred, can you let me know what isn't working on the optimizer? I'll look into it and either provide an explanation or be able to find a bug.