When billionaire Billy Joe "Red" McCombs, co-founder of Clear Channel Communications, reported a $9.8 million loss on his tax return, he failed to include about $259 million from a lucrative stock transaction.

After an audit, the Internal Revenue Service ordered him to pay $44.7 million in back taxes. McCombs, who is worth an estimated $1.4 billion and is a former owner of the Minnesota Vikings, Denver Nuggets and San Antonio Spurs sports franchises, sued the IRS, settling the case in March for about half the disputed amount.

McCombs's fight with the IRS illustrates an overlooked facet in the debate over tax rates paid by the nation's wealthiest. Billionaires — from McCombs to Philip Anschutz to Ronald Lauder — who derive the bulk of their wealth from stock appreciation are using strategies that reap hundreds of millions of dollars from those valuable shares in ways the IRS often doesn't classify as taxable income, securities filings and tax court records show.

"The 800-pound gorilla is unrealized appreciation," said Edward McCaffery, a professor of law, economics and political science at the University of Southern California in Los Angeles.

The rate at which the 400 U.S. taxpayers with the highest adjusted gross income actually paid federal income taxes — their so-called effective tax rate — fell to about 18 percent in 2008 from almost 30 percent in 1995, IRS data show. That's the tip of the iceberg, since much of their wealth never converts into income on a tax return, McCaffery said.

In the McCombs case, the billionaire entered into transactions known as variable prepaid forward contracts. He received about $259 million for lending an investment bank his Clear Channel shares with a promise to deliver the stock for good a few years later. The arrangement enabled McCombs to defer paying capital gains tax because he hadn't sold his shares, lawyers for the billionaire said. The IRS deemed the transaction a sale since the bank paid McCombs cash and got the use of his stock almost immediately.

While the tax treatment of these plans isn't disclosed in the filings, "there's no other reason to enter into such a convoluted arrangement," said Robert Willens, an independent tax accounting analyst in New York. These arrangements can cost several million dollars in fees, according to tax planners.

Taxes on capital gains are triggered when assets like appreciated shares are sold — a process called realization. What constitutes a realized, taxable sale is a frequent bone of contention between the IRS and the clients of tax planners.

Borrowing against appreciated stock and real estate is a popular tax deferral strategy particularly as interest rates plummet, said Randy Beeman, a private wealth manager at The Wise Investor Group. The interest rate on loans to some wealthy individuals has hovered around 1 percent.

In 2010, a U.S. Tax Court judge found Philip Anschutz, the entertainment, oil and media investor, owed $94 million in taxes after he used transactions similar to the ones used by McCombs. Anschutz, identified by Forbes as the 39th richest man in the U.S., is appealing the decision.

The IRS has "gotten more hostile toward these transactions over the years," through its various technical pronouncements and litigation, said Willens, the accounting analyst. Since 2006, such transactions haven't included the interim loan of shares to the investment bank, he said.

"It's still desirable to defer the tax and wind up with an interest free loan from the government," he said. "Chances are you don't get audited and if it does get challenged the odds are good you'll have a settlement for some fraction of the amount you saved. Who wouldn't want that?"