I saw this on Peter's Hyperlipid Blog, and I have no idea what would be causing this phenomenon (someone mentioned trans fats in the comments section), but I got that same spooky "oh, that's not good" feeling I got when I first heard about colony collapse in bees.
If I understand correctly, the usual process of metabolic syndrome and obesity is that the muscle cells become insulin resistant at a faster rate than fat cells. Thus insulin starts rising to compensate for the sake of muscle, but the fat cells, which are still sensitive, take this signal at face value and store more fat. It makes sense that adipose tissue insulin resistance would limit fattening.
I'm guessing that what is damaging the mitochondria is ROSs. Cell membranes are made of highly polyunsaturated fatty acids, which are particularly susceptible to such damage.
My current hypothesis is that people who have difficulty with carbohydrate metabolism are not properly coping with the normal ROS production involved in carbohydrate metabolism. So the inflammation is not being cleared, and it is damaging surrounding cells. Why muscle cells would be more susceptible, I don't know.
This could explain, in part, why switching to a ketogenic diet often and stops and reverses the process -- ketones don't generate as much oxidative radicals when used for fuel, and they are also antioxidative.
Since nobody is answering I'll give my guess. This is called lipotoxicity, where so much fat builds up in the mitochondria that their functioning is impaired. It is caused by an imbalance between the ability to oxidize fat and the need to oxidize fat, which likely comes from a breakdown in the functioning of skeletal muscle uncoupling proteins (UCP3) which assist safe fatty acid oxidation, and that is caused by leptin resistance, since leptin is needed to activate the uncoupling proteins, but if it isn't being registered in the hypothalamus then it can't get to where it needs to go. This is from the book Mastering Leptin and there are some papers on it somewhere.
edit: for typos. From now on I won't paleohack when I really need to go pee.