It's about 95% certain that Karpeles stole the coins, or was involved in a market manip scam to sell them to cover his lawsuits and debts.
He has a history of jail time for financial crimes when he was younger:
http://johnbercow.tumblr.com/post/78352765925/mt-gox-guy-mark-karpeles-went-to-jail-before-forHe also scammed a French out of $30,000, which he used to purchase MtGox.
(the scammee took years to track him down and sue him in Japanese Court, which he won...)
" A 5,000 ($6,870 USD) down payment is placed. Mr. Karpelès returns several months later with bad news. His hired graphics artist failed to complete a subcontract on time, so the first stage of the three-step development process was stall...."
"That was a complete lie. According to court records, Mr. Karpelès could never provide any evidence that there was a subcontractor. By all appearances he had simply taken Mr. Dubois' money, done no work, and then invented a fantasy to cover himself."
http://www.dailytech.com/Bitcoin+King+Mt+Gox+CEO+Mark+Karpels+History+of+Arrests+Firings/article34442.htmhttp://www.dailytech.com/Bitcoin+King+Pt+II+Mt+Goxs+Dictator+Karpels+Proves+Tragically+Flawed/article34452.htm