I have heard about this problem on previous threads.
I arrive in early August but my permit was not issued till end of October 2006. When i applied for my health insurance using comparis.ch they issued my insurance back dated to August 2006. I got one of the Swiss people I work with to call "Avenex" my insurer and told them that I had been covered by my travel insurance and that I couldnt get medical insurance earlier as my permit hadnt been issued to end of October.
They promptly agreed to waiver the premiums and reissued the policy as of 01 November, no questions asked. So the moral of my story is that it maybe worth trying to contact your insurer and explain the situation. Who knows unless you try!