Baylor freshman Perry Jones was declared ineligible by the NCAA on Wednesday after an investigation about whether Jones or his family received preferential treatment or improper benefits from an AAU coach before enrolling in college. The NCAA’s decision came only hours before the Bears played Oklahoma in their first game at the Big 12 Conference tournament. Baylor lost 84-67.

In a release from the school, athletic director Ian McCaw said, “We are profoundly disappointed in the timing and determination in this matter. This outcome appears to be inconsistent with other recent, widely discussed NCAA decisions.”

The NCAA on Thursday responded with its own release:

"Baylor University’s criticism of the NCAA for its reinstatement decision regarding men’s basketball student-athlete Perry Jones is off base, related to timing, process and precedent. In particular, the university denounced the timing of the decision, which occurred just prior to the start of the Big 12 men’s basketball tournament. The university also claimed the decision was inconsistent with other recent eligibility reinstatement decisions.

"In fact, on multiple occasions starting in January, the NCAA notified Baylor University of potential eligibility issues with the student-athlete. It wasn’t until Monday that Baylor declared Mr. Jones ineligible and sought reinstatement from the NCAA. After immediately reviewing the request and also having to seek additional information, the NCAA student-athlete reinstatement staff received the final information it requested Tuesday evening and issued its decision Wednesday morning.

"Regarding comparisons to other cases, each situation is different and has a different set of facts. In this specific case, the student-athlete and his family actually received benefits, including a trip, with the total benefit amount of more than $4,100. This sets the case apart from the Cam Newton case, where there was no sufficient evidence of benefits being provided or direct involvement by the student-athlete."

Baylor’s release said Jones had no knowledge of three, 15-day loans between his mother and AAU coach that were provided while Jones was in high school. The loans were repaid in a timely manner, according to interviews conducted by Baylor officials and the NCAA staff.

Jones’ AAU coach also paid for the player’s travel to a professional preseason football game in San Diego before getting to Baylor, the release said.

McCaw indicated that no Baylor representatives were involved or aware of any preferential treatment between the AAU coach and Jones’ family, whose relationship dates to at least the sixth grade. The AD commended Jones “for being cooperative and forthcoming during this unfortunate process.”

Baylor’s release said the issues that led to Jones’ ineligibility are not considered to be an institutional violation of NCAA rules. That is an important distinction for Baylor, which just last summer completed a five-year NCAA probation period with penalties because of wrongdoing under previous coach Dave Bliss. The program was ravaged in the summer of 2003 by the killing of a player by a teammate, and the aftermath caught Bliss in a tangle of lies and financial misdeeds.

The 6-foot-11 Jones averaged 13.9 points and 7.2 rebounds for Baylor.

The Associated Press contributed to this report.