I found the problem.
Seems that stale certificates have ended up in the mozilla/microb cert8.db file and are causing the errors.
If I move that file out of the way, all the sites that are failing load in microb.
Simply deleting it though isn't the real answer since I dont know what information that file contains. What we need is something that can remove all the bogus certificates from that file (likely bogus intermediate certificates I bet) and "clean" the file up but without removing anything important.