My wife (born in Poland) got some rather rude treatment when we returned from Europe last summer, despite the US passport (nothing as extreme as your mother-in-law experienced).
It is almost as though Customs is deliberately set up to harass the s--- out of citizens and non-citizens entering the country legally while turning a blind eye to illegal Mexicans and suspicious Muslims.
I've always had good experiences with customs officials. I do know the anger associated with dealing with govt officials who could care less about helping you though (dealt with a small town police dept. trying to dispute a ridiculous parking ticket I once received).