I always think it's difficult for a PA as a new employee to learn processes and procedures.  However being that PA, it should be easier to explain it to others.

I agree, speak to the individual and explain that your boss prefers all appointments to be scheduled through you.

For whatever reason, people tend to ignore or disregard emails.  It's much more effective if you speak f2f.  Although the suggestion by Marie of cc'ing your CEO may add some weight.