Lightspeed, a Silicon Valley venture capital firm, was the first institution to invest in Snap, the company that popularized disappearing messages, and it is now set to reap more than $1 billion from what began as a mere $485,000 investment. But the big money for Lightspeed masks a complicated tale between the venture firm and Snap, the parent company of Snapchat. It is a story that offers a peek into the often opaque world of venture capital, into how start-ups begin and into the politics over money that accompany the relationships between companies and entrepreneurs.