Jonathan Ernst/ReutersPhilip Falcone of Harbinger Capital.

Nasty letters from lawmakers. A powerful lobby threatening his very livelihood. Regulatory investigations. These are the things that billionaire hedge fund manager Philip A. Falcone contends with on a near-daily basis.

Today, scorekeepers can chalk up another point for the anti-Falcone factions. His hedge fund, Harbinger Capital Partners, lost 46.6 percent last year, as his biggest — and most controversial — investment took a beating, according to investors who spoke on condition of anonymity.

That investment, LightSquared, is a wireless broadband company racing to bring more than 200 million consumers wholesale 4G wireless access to rival the other major wireless providers. But as a private company, the firm is tricky to value. It does not trade, so there are not many bids on the open market. So auditors have to weigh in with valuations when the firm values its holdings. In December, the firm marked the position down by approximately 50 percent, according to an investor. That came in addition to about a 9 percent markdown earlier last year.

And those valuations do not look pretty, thanks to battles with Washington and others over the firm’s potential interference with GPS signals.

The fate of LightSquared’s wireless ambitions rests in the hands of Washington, which has pumped the brakes hard on the company’s progress. Congressional committees are looking into Mr. Falcone, LightSquared and the Federal Communications Commission, which granted the venture a critical waiver that some consider questionable.

The GPS community, which serves everyone from everyday drivers to emergency vehicle personnel, is up in arms about the venture as well, which also hurts the firm’s valuation. That’s because the spectrum band that LightSquared is entitled to – or the chunk of space where their satellite systems roam – conflicts with those used by GPS providers.

LightSquared says it is entitled to the band it uses, and that GPS has been violating their space for years. Whatever the case, the dust-up pits Mr. Falcone, a relative unknown outside the moneyed club of hedge funds, against some of the biggest forces in the country, like the Department of Defense (which also uses GPS systems).

As such, there is a considerable amount of uncertainty surrounding LightSquared’s viability. And that means whatever the fund had previously marked the company’s worth at was in need of revision. Bloomberg first reported the dire returns.

“The decline was primarily due to a conservative adjustment in the fund’s holdings of LightSquared, to be consistent with the results of work done by the Fund’s third party valuation firm,” a Harbinger representative said in a statement. “The valuation takes into account uncertainty about the outcome of political issues related to alleged interference with the GPS system by LightSquared transmitters. Harbinger continues to work closely with LightSquared to obtain a favorable outcome.”

The investors who remain in the fund are not happy with the results, but at least some who spoke on condition of anonymity saw it coming. One felt that the valuation was overly-rosy for too long.

Investors have fled Mr. Falcone’s fund, which once managed $26 billion, over the last few years as the manager has made a number of blunders. After rising to fame for a prescient bet against the subprime mortgage market, the manager lost big in 2008. He not only refused to let investors redeem their money – he also parked some of his investments in so-called sidepockets, or separate accounts for illiquid positions. The reason: to avoid selling these items into a down market.

As more investors redeemed, Mr. Falcone’s concentration in Lightsquared rose. Now it represents an estimated 60 percent of his fund.

The 2011 performance would be reason enough for a hedge fund manager to be unhappy. But that drop may be the least of his concerns.

Pressure from lawmakers investigating his hedge fund over LightSquared is mounting. And the Securities and Exchange Commission could issue an action against him for allegedly giving Goldman Sachs permission to withdraw money from his hedge fund while other investors could not. The commission is also scrutinizing a $113 million loan he took from Harbinger to pay off a tax bill during the same period.

He’s recently been in the news for a spat with Senator Charles Grassley, Republican of Iowa, who has taken to sending Mr. Falcone letters demanding information and updates on his lobbying efforts on behalf of Lightsquared. Mr. Falcone fired back earlier this week, saying that some of the assertions made about his and his fund were wrong.