In the book he starts out a little more portly and comments about losing weight during the trip to Rivendell with Strider. And it's Gandalf who described him as being "a stout little fellow with red cheeks" "taller than some and fairer than most, and he has a cleft in his chin; perky chap with a bright eye." Gandalf said that to Barliman Butterbeer, describing Frodo as he was just prior to setting out. I think Sam fusses at him about eating on the journey, and I know he was a lot thinner by the time he woke up in Rivendell, but whether or not two months of rest restored some of the weight is not made clear.

Sam, on the other hand, is described as "sturdy" and "brown" (probably from the sun), and his eyes are definitely brown.

To be honest, I'm not in the least offended by this omission in most fic, I just think it's funny.