I love The Lymond Chronicles to death, and while I think that Dorothy Dunnett did a great deal of research, I also believe she took some liberties with the facts for plot reasons. Basically, she needed a highly-placed scheming villainess, and poor Lady Margaret Douglas was her pick. She comes off very badly indeed! Marie de Guise is a minor character in the books; her daughter figures a bit more prominently, though the books end when she's only 16, at the time of her first marriage.
As I said in the Lady Margaret Douglas thread, I put the Lymond Chronicles more in the category of costume drama than historical fiction. In spirit they are much closer to, say, The Three Musketeers than Anya Seton's Katherine. A great read, though.
I'm almost embarrassed to mention Forever Amber in this thread ... but I think Kathleen Windsor did a nice job of portraying Charles II and his milieu. The focus is entirely on his love life as opposed to his policies, but it's a fun read and I don't recall any glaring inaccuracies in it.