The South Bay has all these established players like Google, Facebook, Apple, Yahoo, etc(to name the larger names). San Francisco has the revenue-earners and shit like Clinkle(I guess we have Uber and Airbnb but that story hasn't fully played out yet). Like Square and Dropbox are toast and both SF companies.
I guess it's a small distinction but an important one. The SF tech scene is much, much younger than it's South Bay counterpart.
Clinkle will definitely fail(that is it will never become an established player on it's own like South Bay companies like Apple/Google/Yahoo/etc.). It'll likely be acquired or maybe even crash and burn, regardless I sincerely question it's long-term potential as I do most SF-based tech companies.