Republican appointees on the U.S. Commission on Civil Rights (search) say they have no idea what awaits them when the finances and operations of the commission come to light. Retired Chairperson Mary Frances Berry (search), the 25-year veteran of the group, hasn't audited the commission's books in more than a decade.

"We don't know what we are going to find when we crack open the files, so to speak. We don't even have a good accounting of who works in the building," Jennifer Braceras (search), who was appointed in 2001 to the panel by President Bush, told FOXNews.com. "They, I mean the liberals, have essentially treated us like potted plants for the last several years."

Berry, the often controversial commissioner first appointed to the panel by President Carter in 1980, resigned Tuesday, two days after her latest six-year term expired. The term of her vice-chairman and political ally, Cruz Reynoso (search), expired the same day.

Earlier in the week, the White House had tussled with Berry over her termination date. Reminiscent of an unsuccessful 2002 legal fight in which she refused to seat new Republican appointee Peter Kirsanow (search), Berry insisted, along with staff director and ally Les Jin (search), that the expiration date for their two terms wasn't until Jan. 21, 2005, six years from the day she started her last term. The White House pointed to commission bylaws that said the expiration date is six years from the expiration date of her predecessor's tenure.

Berry, often known for her voracity when willing to wage political battles, decided not to put up a fight over the six weeks, as she explained in her resignation letter.

"Given that the conclusion of my tenure is only a few weeks away, a legal challenge would be an unwise expenditure of resources," wrote Berry, who is registered an independent, but ideologically is a proud liberal. Jin is also out the door.

Republicans often complained that Berry's tenure as chairperson since 1993 allowed her to create a "fiefdom" in which millions of dollars — about $9 million a year for a staff of 70 — went into the commission and were then left unaccounted.

The House Judiciary Committee Constitution Subcommittee two years ago held hearings on the operations of the commission, which has offices in Washington. The Government Accountability Office (search) said in a report a year ago that it had been 12 years since the last audit of the commission and little is known about the panel's financial management.

Kirsanow, also a Bush appointee, said transparency is key. "We are going to insert transparency into not just deliberations of the commission but the inner-workings of the commission's administration," he said. "We want to make the place run the way a federal agency optimally should run."

President Dwight D. Eisenhower established the panel in 1959 to protect the voting rights of blacks as the civil rights debate was just heating up. The commission has no enforcement powers, but has the authority to call hearings and witnesses, hear discrimination complaints and publish reports.

New Staff Director Ken Marcus, a former Education Department official, will join two others — incoming Chairman Gerald Reynolds (search), former assistant secretary for the Department of Education's Office of Civil Rights, and Virginia-based attorney Ashley Taylor (search). Both commissioners were appointed by President Bush over the weekend.

"I know Gerry, he's great," said Abigail Thernstrom, an independent member who was appointed by Congress during President Clinton's administration and sides with conservatives. "He's smart, he's funny and he's going to have an eagle eye for management."

Thernstrom and independent Russell Redenbaugh round off the now six GOP appointees on the eight-member panel. Two Democrats remain — Elsie Meeks (search) and Christopher Edley (search), both of whom could not reached for comment. Thernstrom said the composition of the panel is a "mirror image" to her first days as a commissioner, when Republicans were out-numbered by Democrats two to six.

Nonetheless, officials at the Congressional Black Caucus (search) expressed concern Wednesday about the new makeup of the panel, as well as its new chairman, who they say was opposed to affirmative action policies when he was appointed to his post at the Department of Education.

"The composition of the commission, until recent decades, has always had a record of strong commitment to civil rights law and Supreme Court decisions. The caucus is very concerned that this commitment is now seemingly not apparent," Rep. Elijah Cummings (search), D-Md., chairman of the Congressional Black Caucus, said in a statement to FOXNews.com.

"For example, the proposed new chairman — Mr. Reynolds — was opposed by the caucus when he was nominated to be assistant secretary of education, based on his civil rights record. We will be looking closely to see whether his agenda has changed from his previous record," Cummings said.

Meanwhile, Thernstrom, a social scientist and author of "America in Black and White: One Nation Indivisible," said now is the time for the panel to focus on 21st century problems plaguing civil rights, not getting bogged down in political dogfights and inter-commission wrangling.

"It is the end of an era," said Thernstrom, who engaged in numerous verbal volleys with Berry over the last several years of her term. "I would like to think the commission, in important respects, is going to be much less partisan, much less ideological. [Berry] has been pretty much dictating reports in which the conclusions come first, the evidence comes second."

Berry did not return calls for comment on this story, but Rep. John Conyers (search), D-Mich., told Fox News on Tuesday that Berry had been an effective chairperson who was often targeted unfairly through the years. Still, he said, she persevered and made the commission a testament to the cause of civil rights in America.

"She's going to go down in history as the best civil rights chairperson we've had," Conyers said. "She was under difficult and oppressive circumstances and at the same time she was able to do more with less."

The Republican commissioners have often complained they were left out of the loop on reports, their issues left off of meeting agendas, and their dissent on panel reports left out of final publication. They say the 2001 Florida election report, led by Berry, which found widespread racial disenfranchisement of voters in the disputed 2000 contest between Bush and former Vice President Al Gore, was a classic example of her manipulations.

"During the two Florida hearings, the most basic processes that would have guaranteed a fair and balanced hearing were not followed," Thernstrom testified before Congress in April 2002, complaining that her Republican colleagues hadn't even seen the final report on the election before it was leaked to the press.

But supporters of Berry have often scoffed at conservatives' complaints. During the 2002 hearing before the Constitution Subcommittee, Rep. Jerrold Nadler (search), D-N.Y., said he regarded the charges of fiscal irresponsibility and managerial tyranny against Berry to be the result of "right-wing members who don't approve of civil rights in the Republican Party.

"I see a campaign of defamation against the commission," Nadler added.

Members said they would like to see the panel get away from some of the caustic battles and work on some new issues, like the racial gap in education.

"That doesn't mean there won't be sharp disagreements on some issues — we wouldn't be an energetic or serious body if there weren't — but we will be working toward a common good," Kirsanow said.