we are facing the same issue!
The latest thing we tried was to save the certificate into a file and manually import it. But we have yet to see if this fixes the problem.
It appears that if you want a permanent exception for a certificate, you have to manually install the certificate by following the steps outlined here: https://superuser.com/questions/104146/add-permanent-ssl-certificate-exception-in-chrome-linux
A more convenient solution has been asked for from the development team.