Dear ustczrb,
Worrying about visas feels horrible, I know. I am no expert but it seems unlikely that anyone here would be able to offer advice different to that offered on recent threads like:
http://www.englishforum.ch/permits-visas-government/6401-how-long-do-i-still-need-wait-visa-processing-non-eu.html http://www.englishforum.ch/permits-visas-government/8209-hr-says-my-permit-both-residence-work.html http://www.englishforum.ch/permits-visas-government/7691-how-long-does-take-employer-secure-permit.html Basically you need to call (not email, since you are worried and time is running out) your boss and insist (politely) that he calls the swiss authorities to find out the status of the application. It might be a good idea as well to find out who at the institute is actually dealing with your permit so you can contact them directly. (Perhaps it is your boss himself but more likely a secretary or HR person, I would have thought.) Good luck! W