If he does not sign it, I would sent it to the institute unsigned by him with private letter to institute explaining the situation and give name and phone number of your boss for them to contact him directly if necessary
I would not think it is an issue unless you are short in the area of audit experience
What area does he think you do not have experience in?
ask him to give you work in area he thinks your short in for Nov/dec 10 and file 2010 as one of the experience years
You cant and wont get experience in every area, you would have more work done in say tax or company sec and less audit etc