I can't shake the feeling that it's an answer to the problem "I like the idea of commuting in a shared vehicle, but the bus is dirty and sometimes homeless people ride it."
This is called bus bunching, here's an explanation. http://www.wbez.org/series/curious-city/why-buses-arrive-bun...
Bus bunching is, as that article notes, kind of inherent to the system.
And the obvious solutions (like leapfrogging) drive people crazy. Actually, a lot of Muni's problems relate to "people get really upset when you do the obvious fix". Like reducing the number of stops... good luck with that!
Just two? You've never caught a bus in Chicago then..