Why might those with high general intelligence, or at the top of society, end up not making the world significantly better?

I think the OP's question was intended to be more along the lines of "What stops those with high intelligence from bettering the world ?", Meaning, what gets in the way of the best intentions of the highly intelligent, not why aren't the highly intelligent doing more. The simple answer ? There are so many more stupid people than highly intelligent people that tip the scales in favor of the stupid folk. And that the type of highly-intelligent people who are good at making money (especially off the stupid ones) but suck at being a benefit to the public, also outnumber the more altruistic-minded smart guys. And they really have the money to drag things down and to retard progress.

Because this may not align with their interests. Highly intelligent people have their own interests like everybody, they are not necessarily morally superior. Moreover they are, perhaps surprisingly, as likely to make mistakes as less intelligent people.

Just clarifying your question: when you say "...or at the top of society", are you still referring to intelligence? Anyway, high IQ people commonly have a set of personality traits, such as high moral standards, sensitiveness, no desire to please or bootlick others, no mainstream interests or not being motivated by money, which make it hard for this kind of people to bend themselves to all it takes for one to reach success in our vain shallow self-seeking society. Not all high IQ people who significantly contribute for the world to be a better place become famous worldwide. In fact, many don’t, which makes it hard for us to trust certain graphs… However, Einstein, Mozart, Gandhi, Leonardo Da Vinci, Goethe, Shakespeare, Rembrandt, Copernicus and Edison would be just a few from many names to serve as a proof of how better the world became after their highly significant contributions to humanity.

Intelligence has nothing to do with happiness. Happiness comes from presence and awareness of who one is. Intelligence comes from the mind. Mind's purpose is to survive, not to enjoy. Those with high intelligence might be very good at surviving, which puts them at the top of the society, but that in no way translates to happiness. Happiness is not a function of mind, it exists outside of mind, it happens when the need to survive is outgrown.

The top two reasons I run into. #2. People were not exposed to the ideas, development, opportunity or support, which allows them the means for expanding their learning. This then tends to handicap the persons ability to contribute. #1. The individual is emotionally restricted in some way. This prevents mental resources to be focused on all the dynamics required over time, for true development of something substantial.

I do like this thread,  much to think about. Here's my short answer - Ivory Towers. The cream are skimmed off into elite institutions where diversity of thought and background are either marginalised, ironed out or absent. We then run the risk of ending up with academic thinking that is so divergent from the everyday reality of most people, that it has little chance of being integrated into their daily experience - and therefore fails out in the field. Can we open up education, decision making to those outside academia - and at the same time make sure new ideas are practical and not reinventing the wheel? If so, How?

I am generally considered intelligent. Most of my feelings towards other people, those who need help that is, mainly involve wishing that they would try harder. One time I became a little interested in chess. When I lost, I didn't wish that smart people would write a better guide. Instead, I stayed up until 3 am practicing. This is the reason "smart people" are generally not productive. They get involved in games that affect real life in no real way (called "pushing wood" by people who don't appreciate the subjective beauty of chess) and just get absorbed. Imagine if Bobby Fischer became a rocket scientist. There would be tons of new stuff for rockets and traveling to Mars and such. Generally, when smart people don't produce anything in any one field, it's due to too many hobbies grabbing their attention. That's what smart people do. They have thoughts. Most require that their thoughts have a connection to real life (whether on a chess board or on a piece of paper, or in the form of a business). Tl;dr Smart people will always be thinking. The problem is that they may not channel it toward anything useful or channel to too many things.

Intelligence is a tool. More intelligence is a better tool. Having a better tool doesn't mean you will make better use of it.

Nice question. I think Maslow's hierarchy of needs may provide some insights over here. http://en.wikipedia.org/wiki/Maslow's_hierarchy_of_needs You can question the accuracy or credibility of this, however, it does give you a start, something to think about. Building on this argument, 'Self-actualization', what you seem to refer to as substantive contribution is the last thing an individual will hope to acquire. I am not sure where I would place IQ in this hierarchy, but for the sake of this argument I would tend to place things like knowledge (which is acquired) and intelligence (which is cumulative) in 'Esteem', just before 'Self-actualization'. The driving force for acquiring such things could also be self-gratification, and the distance between Esteem and Self-actualization is rather huge. An individual would make the leap into the next level only after fulfilling the level below. Gaining Esteem, a sense of achievement, is highly competitive and when the bar keeps rising constantly, the barrier to entry to the next level raises progressively. Another reason why it seems tough to jump from Esteem to Self Actualization is because from this point onwards the sense of purpose shifts away from the self.