Amid a controversy over its practice of allowing some employees to cash large checks for unused leave time at retirement, the state Department of Public Safety and Corrections has decided to cap future payouts at 20 days’ salary.

The policy change apparently won’t apply, however, to former Louisiana State Penitentiary at Angola Warden Burl Cain, who retired effective Jan. 1 but is set to collect his regular paycheck through Aug. 31.

Cain’s eight-month payout was approved under the previous rules, which gave the department head — in this case Cain’s boss and close friend Jimmy LeBlanc — complete discretion in deciding how much unused leave to allow a retiring employee to “burn.” Cain will collect approximately $134,000 in salary over that period.

“The new policy applies to all employees but cannot be applied retroactively,” said Pam Laborde, spokeswoman for the department.

The new leave policy was being distributed this week amid another shake-up in the department, one that has led to the temporary removal of Burl Cain’s son, Nate, as warden of Avoyelles Correctional Center, a position he has held since 2012.

Department officials offered few new details Thursday about that probe, which they have described as an investigation into “personnel issues.”

Sources with knowledge of the matter said that in addition to Nate Cain, two other employees of the Cottonport prison have been placed on leave: Tonia Cain, the warden’s wife, who until recently was the prison’s business manager, and Paul Gaspard, a deputy warden.

Laborde declined to answer questions about the job status of Gaspard or either of the Cains, saying only that all three remained employed by the corrections department as of Thursday. She also declined to address questions about whether Nate and Tonia Cain’s work computers had been seized by investigators.

It’s unclear precisely what the internal probe at the Avoyelles prison centers on. It follows a number of public records requests filed by The Advocate seeking credit card receipts, ledgers showing money taken in by inmate concessions and invoices for a new building inside the prison’s gates.

The newspaper has received only a portion of those documents, which it requested after receiving tips about misspending and other possible misconduct.

The department’s investigation into the Cottonport prison comes amid widespread questions about its handling of allegations concerning Burl Cain, particularly whether the longtime Angola warden violated a rule barring “nonprofessional” relationships between correctional employees and inmates’ relatives and friends.

The department’s investigation essentially cleared the elder Cain, saying that the ban was aimed at sexual relationships, not business deals like Cain’s real-estate ventures.

In response to questions posed by The Advocate, a spokesman for Gov. John Bel Edwards said the governor “has complete confidence in Secretary LeBlanc and the department to conduct a thorough investigation. If he didn’t, he wouldn’t be leading the Department of Corrections.”

State Rep. Kenny Havard, R-St. Francisville, an outspoken critic of Cain who has said he thought the investigation into the Angola warden’s actions was handled poorly, said he has higher hopes for the probe of the younger Cain.

“In my opinion, they haven’t proven they can” conduct a fair probe, Havard said. “But hopefully, with all the light shining on what a lot of people consider a shoddy investigation of Burl, they’ll do a more thorough job this time.”

Follow Gordon Russell on Twitter, @gordonrussell1.