This may be rehashed, but I just noticed this when watching ROTS this week.
It has been mentioned in many sources that the Order 66 was a trained order, not brain washed. It might have been in SWInsider that it was said that the Clones are loyal to the Republic and that is why they did it without question.
BUT.....why did they immediately start referring to Palps as "Lord"? I was under the impression from the previous two prequels that the title "Lord" was used only to the Sith?