Seeds can go bad. One way to check their quality is to sprout some of them. If less than 50% germinate they're past their prime.
It's an all seed diet that frequently leads to liver disease, not pellets. It's really a malnutrition issue not something directly caused by the seeds themselves. The usual pattern is that birds eat excessive amounts of seed trying to get nutrients that aren't plentiful in seed, which leads to fat buildup in the liver.
Pellets aren't expected to cause malnutrition problems, but too many pellets can cause kidney disease in sensitive individuals when pellets are 90% or more of the diet. The cure for it is to lay off pellets for a while and then add pellets back to the diet at a lower percentage, according to Chapter 16 at this link:
http://avianmedicine.net/publication_ca ... -medicine/Pellets don't contain excessive amounts of protein since they have been formulated to provide an appropriate amount that is not too much or too little. There's an acceptable range of values and the protein and fat content varies between brands. A study on cockatiels found that they could live on a diet of 70% protein for 11 months without any problems.
http://jn.nutrition.org/content/131/7/2014.short The study was probably intended to find out how much protein was too much but they never did find the upper limit lol. The protein percent in pellets is nowhere near that. Most regular pellets have protein in the 12-15% range.
If you prefer for the protein and/or fat percentage to be higher or lower than average, you can compare brands and pick the one whose numbers you like best. My article has a chart showing the protein and fat percentages for several brands, and you can compare any other brand to this to see whether it's in line.
Lafeber is an excellent company. The original Dr Lafeber invented pellets to deal with the terrible malnutrition problems he saw in his patients back in the 1970s, and now his son (also an avian vet) runs the company. The company continues to do research into bird nutrition and other issues.
http://lafeber.com/our-story/People who are emotionally attached to certain ideas about nutrition tend to dislike Lafeber because it's not organic, it contains a small amount of sugar, and it uses artificial preservatives. If you've read my article you know that NONE of this is actually meaningful. Organic and conventional are basically equal in terms of nutritional value and safety. The amount of sugar is small and doesn't have a significant effect on the glycemic load or anything else. The preservatives are safe, and eating them is far better than eating food that went bad because preservatives weren't used.