That’s one surprising conclusion from Glass Lewis’ latest report on executive pay. The proxy adviser rates the 25 most overpaid and underpaid chief executives at S&P 500 companies, based on changes in stock price, book value, operating cash flow, earnings, total shareholder return and the return on assets and equity. Glass Lewis repeated the exercise at the smaller companies in the Russell 3000 as well.

In general, Glass Lewis says, companies on the Underpaid 25 lists “substantially outperformed their Overpaid 25 counterparts, as well as paid their top executives far less in total compensation.”

The average S&P 500 company on the Underpaid 25 list, for instance, posted $1.26 billion in net income and showed 60% earnings per share growth. The average S&P 500 entrant to the Overpaid 25 list, by contrast, lost $373 million and posted an arithmetic-defying 101% decline in per-share earnings.

Meanwhile the median pay for the big but underpaid group, led by Amazon’s Jeff Bezos, Apple’s Steve Jobs and Goldman Sachs’ Lloyd Blankfein, was $3.4 million. That’s not exactly peanuts, but it’s less than a third of the $11.7 million comparable figure for overpaid big-company CEOs typified by Sprint’s Dan Hesse, who has made the list an impressive three years running.

Yet there is one area in which the overpaid CEOs clearly did better: The average S&P 500 company led by an overpaid CEO posted a 59% stock gain last year, compared with a 54% gain for those led by an underpaid CEO.

Obviously, a five-point spread doesn’t make shareholders rich beyond their wildest dreams or excuse the boards that are merrily squandering scarce corporate resources. Glass Lewis says it produces the report in part to identify companies “whose compensation practices may expose shareholders to undue risk.”

Still, what’s going on here? You could argue the surprise is an artifact of timing: the report covers fiscal 2009, in which stocks plunged early in the year before bottoming in March. They then took off in near vertical fashion, with the biggest gains concentrated among the riskier players — the so-called junk rally. It stands to reason that if you were going to average a $373 million loss, this might well have been the year to do it.

But the outperformance of S&P 500 fat cats wasn’t repeated by their overpaid compatriots in the small stock sample of the Glass Lewis report, the Russell 3000.

In that case, the median overpaid CEO drew $6.9 million in compensation — more than 11 times as much as the median underpaid chief. But companies led by underpaid CEOs, such as Daniel Baker of nanotechnologist NVE , posted an average stock gain of 143% — more than triple the gain of overpayers such as NCR , the automated teller machine company once headed by Mark Hurd and now piloted by former Cisco exec Bill Nuti.

So the mystery of the S&P 500 fat cat gap remains. Nuti, for his part, received* $7 million in 2009 —  a year in which the company deserted its longtime home base of Dayton, Ohio, lost $33 million and saw its stock drop 21%. For one man, at least, NCR truly is a cash machine.

*Update Oct. 18: NCR takes issue with my original phrasing, “took home,” because Nuti didn’t take a lot of it home. Indeed, a spokesman says Nuti relinquished about half of the indicated $7 million as a result of the company’s failure to meet performance targets.

Fair enough. So Nuti ended up taking home a measly $3.4 million for a year in which the company and its shareholders both lost millions. That’ll teach him.