A. Whereas on many petty issues that were not very important for the company’s future, the board members could not come to an agreement, some major issues were agreed unanimously.
"Some major issues were agreed unanimously" we are not given who did the agreement
B. Whereas about many petty issues that were not very important for the company’s future, the board members could not reach an agreement, about some major issues they agreed unanimously.
CorrectC. Unlike many petty issues not very important for the company’s future, on which the board members could not come to an agreement, they agreed unanimously on some major issues.
Wrong comparison "Unlike many petty issues... they" we are comparing petty issues to board members
D. Unlike the agreement that the board members could not reach on many petty issues that were not very important for the company’s future, they agreed unanimously on some major issues.
Wrong comparison "Unlike the agreement... they" we are comparing an agreement to board members
E. Although the board members could not come to an agreement with many petty issues that were not very important for the company’s future, they agreed unanimously to some major issues.
This would be perfect had we used "come to an agreement on" instead of "with"; you agree with "human beings" whereas you agree on "non-persons" (ideas, issues, etc..)