Remember the Year of the Whistleblower, when insiders in government and industry made magazine covers? Those were the good old days.

These days most whistleblowers are back to being persona non grata. Probably no one knows that better than the U.S. serviceman who blew the whistle on prisoner abuses at Abu Ghraib in Iraq. A lot of good it did him.

Whistleblowers have not only been given the impression that they should butt out, but some are getting a good swift kick from Uncle Sam. Some have alleged retaliations and seen their disclosures thrown out without comment by the federal government. However, some advocacy groups are working in the public interest and against government secrecy. They’re making a stink big enough for even Congress to smell. That’s good because there is something rotten in Washington, and it’s getting worse.

The American Civil Liberties Union and the Project on Government Oversight have taken on the U.S. Special Counsel, alleging that the office charged with protecting federal whistleblowers isn’t. Both have gone to court to get records open.

The advocacy group Public Employees for Environmental Responsibility has lambasted special counsel Scott Bloch over the dismissal of 600 whistleblower cases. Questions have arisen about why these cases were dismissed and whether they were dismissed unlawfully. There are also questions about whether taxpayers’ money is being wasted. The Washington Post reported that most of the cases dismissed under Bloch involved federal employees who had reported waste, fraud and other abuse. Yet in many instances, whistleblowers weren’t told why their disclosures were thrown out.

Bloch’s office has gotten attention from U.S. Reps. Henry Waxman and Danny Davis, members of the House Government Reform Committee, who called on the Government Accountability Office to investigate. Besides the hundreds of dropped cases, Waxman and Davis want the GAO to consider “Bloch’s forced removal of OSC staff, hiring of cronies and failure to answer Freedom of Information Act requests.”

Some in the OSC had complained about the erosion of whistleblower protections and alleged they were subjected to reprisals for having done so. How ironic! Bloch denies any wrongdoing, contending that he has made the office more efficient.

Congress is attempting to close loopholes in whistleblower protections. Sens. Daniel K. Akaka, a Hawaii Democrat, and Susan Collins, a Maine Republican, recently reintroduced their Federal Employee Protection of Disclosures Act.

It seeks to encourage more civil servants to report waste, fraud and abuse by clarifying the Whistleblower Protection Act of 1989. The U.S. Special Counsel would be given authority to file in federal courts amicus briefs supportive of whistleblowers. This public push to get more civil servants to tell what they know conflicts with whistleblowers’ private experience: no good deed goes unpunished.

In March, the Justice Department admitted it retroactively classified information, including use of the “state-secrets privilege.” Reportedly, the Justice Department in May 2004 “classified” information which the FBI provided to the Senate Judiciary Committee two years earlier at “unclassified” hearings. The public learned of this through a lawsuit that the Public Employees for Environmental Responsibility filed against the Justice Department.

The ACLU contends that the government willfully stalled the case of FBI whistleblower Sibel Edmonds, a former translator. Edmonds revealed serious gaps in intelligence gathering during the war on terrorism. She alleges her free-speech rights and right not to be punished are being violated. The government alleges “significant damage to the national security and foreign policy of the United States” were her case to proceed. To the ACLU, this issue is bigger than one FBI translator. It’s “part of a larger pattern by the government to silence employees who expose national security blunders.” It’s about the arrogance of power.

Speaking of blunders, a presidential commission last week issued a 601-page report on “poor tradecraft and poor management” in the terror war. “We conclude that the intelligence community was dead wrong in almost all of its prewar judgments about Iraq’s weapons of mass destruction,” the panel wrote in its unclassified report. “This was a major intelligence failure.”

This war is a failure on many levels. Yet what incentive is there for people to report mistakes?

More bad news: The Defense Department’s inspector general found that last year 671 U.S. troops – up from 597 in 2003 – complained of reprisals for disclosing waste, fraud and abuse. Twenty-three allegations were substantiated; 40 the year before. Want to really support the troops? You do the math. Some things don’t add up.