As I know, your university must fall under Public or Non-profit Institution. Last year when i was filing for the master cap, i had same situation whether to file for masters Cap (Advanced Degree Exemption) or for the regular cap.

Institution Must be Public or Other Nonprofit Institution

Under the law, the beneficiary's U.S. degree must be issued by an institution of higher education that is "a public or other nonprofit institution." The institution must also be "accredited by a nationally recognized accrediting agency or association" or "granted a pre-accreditation status."

As such, problems arise when the institution issuing a beneficiary's advanced degree is a for-profit and/or an unaccredited school. Degrees from such institutions do not meet the master's cap statutory requirement and, therefore, cannot serve as a basis for an H1B petition requesting one of the 20,000 such exemptions from the regular H1B cap. Current USCIS practice for cases filed under the master's cap without a qualifying degree is to deny such cases, rather than consider them under the regular cap.

Reference : 

http://www.murthy.com/2012/11/19/requirements-for-u-s-masters-graduates-to-enjoy-benefit-of-h1b-masters-cap/