Box’s market cap is $2.5 bil, so that’s still $85 mil. If he can take actions that increase their market cap 10%, that’s still $8.5 mil for him personally. I feel like his interests are still very aligned with “grow Box”, even if he isn’t given more equity.

True, but he could always divest before leaving. In theory that seems like the right move if he's undercompensated, assuming that his motives are purely financial, that the market has valued the company correctly, and that his career won't suffer from "quitting".

What's the story behind how he ended up with only 3.4%? Just lots of dilution, or something more unusual?

I believe he was 1 of 4 co-founders, and then raised 11 (according to crunch base) financing rounds. If you get diluted even a very reasonable amount 11 times, you won't end up with a large percentage of the company.

Basically if a company is successful they'll probably raise many rounds and then end up with their founder/ceo only having a small portion of equity. At this point, the founder/ceo might be rich and has "made it" so could easily leave and be happy, but investors may want them to stick around. One way to get them to stick around might be to compensate them with even more stock.

Obviously depends on the situation, but it seems silly to lose a founder/ceo because investors didn't want to dilute their equity and give the founder/ceo a little more.

I believe he was 19 years old.