getcanada,
It is a rare case that VO gets confirmation form the university in regard to genuineness of degree awarded to the PR applicant.It is inconceivable as to how could the university authority pass comment which is contrary to otherwise genuine certificate issued by it.
However,if u feel that there is some communication gap that might have crept into, u could write to the university authority by apprise it with VO'S CLAIM nd request to issue an amended letter to VO explaining therein the mistake committed in the process. Make sure to endorse this letter to VO, as well. Get a certified copy of this letter from university nd send it to VO WITH UR EXPLANATION.
Hope, this should help dispersing the clouds of confusion.
Good luck nd May God bless all !!!!
parhar51