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Do not confuse a strong letter of reference for a top-flight MBA program with a strong letter of reference for a top-rankedprogram. Each program is very different from the other with different objectives in mind - in particular, what each type of program views as the "ideal" candidate is often very different from the other.
If you are applying to a top-tier PhD program in business (such as Fisher's program), your references must be able to comment on your potential for being a scholar who can do independent research in that particular field of study. Most times, academic references carry more weight in the admissions process for PhD applicants. An exception can be made for non-academic references if those non-academic references can comment on the applicant's potential for scholarly research. Key to remember is that each of your references must know you very well, well enough to know your strengths, weaknesses, etc., at such a level of detail that s/he can state unequivocally that you are well suited for PhD studies.
If you have any questions on the PhD application process, please let us know.