WACO, Texas -- A player missing and presumed dead. A former teammate jailed on murder charges. And now this.

Already reeling from the saga surrounding basketball player Patrick Dennehy's disappearance, Baylor's beleaguered athletic department faced questions Wednesday about whether coaches made improper payments to Dennehy.

While lamenting the timing of the allegations, Baylor Athletic Director Tom Stanton said the university "has begun a vigorous internal inquiry independent of the athletic department to determine the facts in this situation."

"The investigation will be thorough," Stanton said. "We take these issues very seriously. We are hopeful questions about Patrick's first year at Baylor can be resolved quickly."

Dennehy, 21, has been missing since mid-June. Former teammate Carlton Dotson has been charged with murder, accused of shooting him in the head. Police haven't found Dennehy's body.

Among the allegations against Baylor is that Dennehy emerged from basketball offices last November with between $1,200 and $1,800 that he told his girlfriend, Jessica De La Rosa, came from a coach and was to go toward the purchase of a car.

The 6-foot-10 center's father, Patrick Dennehy Sr., said in published reports that De La Rosa, a University of New Mexico track athlete, reported what she saw to officials at New Mexico and that they reported it to the NCAA.

The NCAA, a governing body for college sports, prohibits extra benefits to athletes. It's the organization's policy not to confirm or deny whether a school is under investigation.

De La Rosa, who was in Waco on Wednesday with Dennehy's mother and stepfather, confirmed she spoke to New Mexico officials but declined to comment on what she said.

Dennehy Sr. also said a member of Baylor's basketball staff paid a car service to drive De La Rosa from Waco to a Dallas airport last fall. That allegation was investigated by New Mexico and the NCAA, and De La Rosa was declared ineligible to run track next season. She likely will be reinstated if she repays the cost of the trip, said Janice Ruggiero, a New Mexico athletics official.

Dennehy's father, who lives in Tacoma, Wash., had been estranged from his son until the last few years. He said he was just now speaking up about the alleged financial favors because he was frustrated with Baylor for not keeping him informed about the investigation into his son's disappearance.

He said a Baylor coach helped arrange to pay for his son's education and living expenses when the player agreed to give up his scholarship to another player last year. After transferring to Baylor from New Mexico, Dennehy had to sit out last season because of NCAA transfer rules.

Dennehy Sr. said the coach promised to "take care of" his son. If the younger Dennehy wasn't on scholarship, he would have been responsible for tuition and other expenses.

The player's mother, Valorie Brabazon, identified the coach as assistant coach Rodney Belcher. Brabazon told The Dallas Morning News for a story in Thursday's editions that Belcher also drove her son from Albuquerque to Waco last year when he transferred -- which would be a violation of NCAA rules.

Dennehy's stepfather, Brian Brabazon, said his wife was unavailable for comment Wednesday night. He declined to comment.

"This isn't going to help us find Patrick," he told The Associated Press. "We have more questions than we have answers. I don't want to be talking about that."

Valorie Brabazon also told the Morning News that, after her son disappeared, De La Rosa told her that Belcher was one of at least two Baylor coaches Dennehy went to this spring to say he was being threatened.

"I talked to Coach Rodney," the mother said. "He said Patrick had come to him and said that someone was stalking him. ... But the coach said my son never gave him a name.

"The coach said Patrick didn't ask him for help. But I said, 'That's a help-me call.' You shouldn't have to say, 'Could you please call the police?'"

Belcher, who coached at New Mexico during Dennehy's time there, could not be reached for comment.

Baylor coach Dave Bliss has said no one on his staff was informed of threats against Dennehy.

Through an athletic department spokesman, Bliss and his staff denied the allegations -- which could constitute a violation of NCAA rules.

"It is unsettling to learn about these assertions and rumors against Patrick and the university at this particular moment when Patrick is not here to give his side of the story," Stanton said in a written statement. "Patrick's reputation is important to us, and the reputation of our athletic department and its coaches is important to us."

Dennehy's mother and stepfather have said that they couldn't pay his tuition, living expenses and car payments.

Valorie Brabazon said her son, soon after arriving in Waco last year, asked her to fill out forms to help him apply for financial aid. She said the family learned later that the application was rejected because their income was too high.

She said that her son ultimately told her the school had helped him arrange to get tuition money and that she assumed it came from grants and loans.

Grant Teaff, executive director of the Waco-based American Football Coaches Association and a former Baylor football coach, cautioned against a rush to judgment about Dennehy receiving money from a coach.

"I would be not only surprised, I'd be quite shocked," said Teaff, who coached 21 years at Baylor and served 12 years as chairman of the football coaches association's ethics committee.

"I knew Dave Bliss when he was at SMU through our coaching contacts and with him now living here in town, and I've never heard any indication of anybody doing anything out of line," Teaff said. "Of course, I'm not in a position to hear everything."