For example, in all three years that I took chemistry I never once got an A in that class; a result that is completely contrary to my standardized test scores (AP/SAT/IB). But eh, as a wise negro once said, "in order to survive, you got to learn to live with regrets."
In college, the same problems arise. But you're going to Stanford, so you probably won't run into them. I apparently know nothing about triple integrals.
Ugh... every time I walk into the administrative building on campus I know I'm going to come out with either the answer I didn't want or no answer at all. The most frustrating thing for me is always going in, explaining my situation to 3+ people just trying to find the right person to talk to, and when I finally reach that person, he/she is incredibly rude and won't even listen to the whole story. Part of my story doesn't sound right, and I hear, "No, that's impossible. I'm glad I could help." Of course, I always thank them for their time, and then go about my scheming to figure out how that no really meant yes.
The trick is resort to using the giant administration as a last ditch effort. It's much easier to get things done informally with advisers, department heads, and individual professors.