During a critical period between 2000 and 2001, decisions on stock options grants at Apple ( AAPL) were made not by an independent committee of directors but by the company's board -- and potentially, CEO Steve Jobs.

Such decisions at Apple, including who receives options and their grant date, are usually overseen by a compensation committee comprising two to three independent directors. Some Wall Street analysts have suggested that bureaucratic layer is why Jobs won't be implicated in the company's ongoing probe into "irregularities" it has found in options grants made between 1997 and 2001.

"Even in the worst-case scenario where AAPL is found guilty of granting options improperly, we do not believe Steve Jobs is liable," wrote Shaw Wu, in a research note in late June, immediately after Apple first revealed its options problems. "The reason being the compensation committee at AAPL is run by an independent board who are not employees of AAPL."

But that hasn't always been the case. From April 2000 to August 2001, Apple's board didn't have a compensation committee, according to the company's regulatory filings. Instead, decisions about options grants and executive pay were left up to the board itself.

At that time, Apple's board included at least two directors that the company itself didn't consider to be independent, Jobs and Jerome York, who was then CEO of MicroWarehouse, an online and catalog retailer that accounted for about 2.9% of Apple's sales in fiscal 2001.

The extent to which Jobs participated in board discussions about options during that time period is unclear from Apple's filings. In a proxy statement filed in March 2001, which covered the company's fiscal year ended in September 2000, the company said Jobs "does not participate in deliberations of the board concerning executive compensation."

But the company did not clarify whether Jobs recused himself only from discussions about his own pay as CEO or from all discussions about compensation for top-level management or options grants to them.

And the following year, in a proxy statement which covered the fiscal year ended in September 2001, that caveat isn't there.

Indeed, the second proxy document appears to contradict the first: "From April 2000 until August 2001, the entire board of directors acted with respect to matters previously considered by a compensation committee," the company said in its latter regulatory filing.

The revelation that Apple didn't have a compensation committee during that 16-month period removes one more fig leaf separating Jobs from at least some of the company's questionable options grants, notes Paul Hodgson, a senior research associate at watchdog group The Corporate Library.

"That defense seems to be on somewhat shaky ground," says Hodgson, who has been covering the growing, broader scandal involving stock options backdating .

An Apple representative did not comment to a request for a clarification about whether Jobs participated in board discussions about options grants during that 16-month time period. Apple's board members during that time period, including York, also did not respond immediately to calls or email messages seeking comment on Jobs' role during that period.

At the company's developer conference this week, Jobs himself declined to comment on his knowledge about the company's options problems.

Apple handed out just one bunch of options grants to top executives between April 2000 and August 2001. While Jobs did not receive any options in that round of grants, which the company gave out in January 2001, it was still sizable and significant.

In that round, the company gave out a split-adjusted 2 million options each to four executives: CFO Fred Anderson; Timothy Cook, then the company's executive vice president in charge of worldwide sales and operations; Jonathan Rubenstein, then the company's senior vice president in charge of hardware engineering; and Avadis Tevanian Jr., then Apple's senior vice president in charge of software engineering.

As The Wall Street Journal reported earlier this week, that grant looks somewhat suspect in retrospect given how very favorably priced it was.

The strike price of the options handed out in the grant was equal to the market closing price of Apple's stock on Jan. 17 that year. After the market closed, Apple reported its first-quarter earnings that year. In reaction to that news, the company's stock shot up 11% the next day, giving the four executives a paper gain of $1.9 million each. Three months later, Apple's stock was up 21%.

Further, while the company was likely keeping with the regulations in place at the time, it apparently didn't report the grants until 11 months after the fact. The first mention of the grants in a search of the Securities and Exchange Commission filings is in the company's annual report filed in December 2001.

In addition to the options grants, at least one other executive compensation decision made in about the same time period stands out. At some point in fiscal 2001 -- Apple didn't specify the exact date in its filings -- the company transferred to Jobs' control of an airplane bought on his behalf in late 1999. The company assessed the plane's value at the time at $43.5 million, which Jobs reported as a bonus.

The company also gave Jobs another $40 million that year to pay taxes associated with the airplane.

Apple is only one of dozens of companies that are under investigation for their past options grants. In general, the probes are looking into alleged misdating of options grants, particularly backdating. With backdating, corporate insiders are accused of retroactively assigning to options a grant date on which their company's stock was known to have hit a short-term low.

Thus far, the probes have led to criminal indictments of former executives at Brocade ( BRCD) and Comverse ( CMVT). Options troubles at those and other companies have led to the ouster of executives and board members, and have prompted shareholder suits.

The myriad investigations have been thought to be a significant contributor to the summerlong sluggishness in tech stocks; even shares of Apple have recently slumped to give back about half of their post-earnings report bounce from late July. The stock closed Wednesday down $1.19, or 1.8%, to $63.59.

Apple has not elaborated on what kind of, or how many, "irregularities" it has found in its past options grants. However, Apple is the subject of several shareholder suits related to the matter, and the company said last week that what it has found thus far will force it to restate its earnings for fiscal years 2003 through 2005.

Another company whose options have drawn scrutiny of late is Pixar , the animation studio formerly headed by Jobs that Disney acquired earlier this year. The Journal reported on Wednesday that, similar to Apple, decisions about options at Pixar during part of the period in question were made repeatedly by the company's board, of which Jobs was a member, and not by an independent compensation committee.

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