Where are you from?
I applied for my student visa rather late (I'm from Canada), but was able to start my studies on time. I simply came to Switzerland as a tourist shortly before my classes started, while my visa was still being processed. I did not have to show my visa when registering at the university - nobody asked any questions, and as far as I have been able to find out, it's not illegal - either that or nobody cares about it. Then when my visa was finally ready I explained the situation to the embassy in Canada, and they sent it to Stuttgart where I could pick it up. (They couldn't send it to Switzerland, because in order to acquire a visa you can't be within the country.)
I study in Zurich, so I'm not sure whether they're as lax in Bern. But I had many, many phone conversations with the university's registrar office before arriving (since I was in a panic about the visa), and they told me it shouldn't be a problem.
And it wasn't!
Good luck!
Juliet