I took a course in my Master degree and I got (B). After I got my degree I applied to the Phd program in the same campus. When I started my Phd program I retook the course and got (A). I submitted my plan of study for the PhD and it was approved by my department. However, the grad school rejected my plan of study and wants me to use the old grade since it was used in the Master. They don't want me to use the new grade at all. The (B) will affect my GPA and I'd have to take another course to meet the required GPA.
I want to know, why the grad school rejected the repeated course? and what should I do?