Pasting from an earlier comment:
One big difference is that NetMarketShare tries to measure unique clients, while StatCounter measures web page hits.
Since the power users browse (probably a magnitude of order) more web pages than the normal users, Chrome and to a lesser extent Firefox is overrepresented in power users who browse a ton.
Toothpaste marketshare analogy. It's possible that 70% of people use Colgate and 30% use Crest, but Colgate sales by volume are only 40% vs. 60% for Crest, since Crest users tend to brush more daily and use more of the toothpaste when they do for some reason.
Or a car analogy: Toyota sells 40% of cars and Honda only 30%, but 60% of miles driven on roads are by Honda cars since they use it more. Which has a higher marketshare?