The remaining 93.9% belonged to the founders, the Board, the employees, and friends and family. Everyone listed on the S-1, with one exception, took a bit off the top but held on to most of their shares.
The one exception was Bill Gates's sister's trust fund, which owned 20,000 shares -- 0.1% of the company. She could've been a hundred-millionaire if she'd held on to it, but her trustee sold it for $400,000 and moved on.
Realize they've raised at least $414M that has been reported.
At many of those rounds it was likely possible for founders/ early employees to cash out options. FB/ Mark had enormous leverage because it was an unstoppable growth machine. Box is a great company, but still has to battle to grow sales into revenue/ profits, as is evidenced by the S-1.
Gates had 45% of Microsoft the day after their IPO. Larry Ellison still owns ~20% of Oracle. Google's founders still have ~10%. David Filo even still has around 9% of Yahoo (Yang & Filo had closer to 20% at the time of the IPO if I recall). Bezos still has around 18% of Amazon. When Dell IPO'd, Michael Dell still owned a huge percentage of the company at IPO, over 40% if I recall (he sold most of it high, which is why before they took Dell private, he was nearly worth more than the company).