Last week, Clemson University found itself on the losing side as U.S. District Senior Judge Matthew Perry refused to dismiss a federal lawsuit against the school brought by the recently terminated executive secretary to its board of trustees.

Eugene Troutman, who served the board for over two years, alleges in his suit that Clemson has accumulated a “rainy day” fund of unrestricted cash worth nearly $80 million since 2000 while simultaneously raising tuition rates and begging the state General Assembly for more funding.

Substantial tuition increases have been the rule nationwide over the last 20 years as the pool of governmental monies available to higher education shrinks due to more reasons than there’s space here to list.

Troutman also alleges that cash reserves were deliberately hidden from the General Assembly, pay raises were given to university officials close to President James Barker, and Board of Trustees Chairman Bill Hendrix kept financial reports from his fellow trustees.

Troutman, who was also an assistant to Barker, asserts that he received only positive job evaluations before he raised questions about the funds and sought to form an audit group. He said he was asked to resign and sign a nondisclosure agreement last summer after urging the board to spend down the cash reserve and open up the school’s financial practices.

The 49-page lawsuit also details Troutman’s allegations that the board publicly impugned his integrity following his dismissal, with Hendrix characterizing Troutman as a “disgruntled former employee” to media outlets.

Alone among South Carolina’s public colleges and universities, Clemson’s board of trustees includes seven life members who are self-appointed and self-governed. Six other members are chosen by the General Assembly, but sometimes the Governor’s Office gets thrown a bone in the selection process.

University spokesperson Cathy Sams said Troutman was fired last August for “management and work style” concerns following a unanimous trustees’ vote.

Judge Perry — he was Harvey Gantt’s lawyer in the 1963 desegregation case against the school — ruled in the suit’s first hearing. He said, “At this point, I am unable to conclude the plaintiff can prove no set of facts that would entitle the plaintiff to some relief.” Perry also let stand the defamation charge and denied Clemson’s request to hear the case in the Upstate.

Sams issued a statement for Clemson, saying, “We are prepared to move to the next phase where we will have an opportunity to respond to the allegations in the complaint, which are completely false and without merit.”

Sams also denied Troutman’s allegation about the $80 million, claiming that even though the funds were “unrestricted,” that doesn’t mean they weren’t budgeted.

Clemson responded to Troutman’s filings by saying that he failed to establish “an effective working relationship” with the board and that he was “improperly circumventing” the trustees’ policy protocol by seeking auditors.

Also cited by Clemson is a 2006 U.S. Supreme Court decision that public employees are not protected by First Amendment guarantees when they make allegations about their employer.

Joel Collins, Troutman’s lawyer, responded that his client’s alerts about fiscally unsound behaviors were outside the scope of his employment and were done as a citizen. Collins also says Clemson can’t have it both ways; the school can’t claim Troutman was let go for “doing too much” outside his job and then assert that everything Troutman did was within the scope of his employment.

On the same day as the hearing, Clemson announced that it was handing out pay raises of $140,000 to nine assistant football coaches. The salaries now range from $110,000 for tight end coach Billy Napier to $260,000 for defensive coordinator Vic Koenning. Four assistants now make over $200,000 annually.