Anderson, Apple’s CFO for many years, yesterday agreed to pay $3.5m to settle charges that he was involved in backdated stock options grants that were incorrectly accounted for.

After the settlement with the Securities and Exchange Commission, he issued a statement through his lawyer, suggesting Jobs had misled him in 2001 about the legitimacy of the grant dates.

Apple’s board of directors, which includes the likes of former US vice president Al Gore and Google CEO Eric Schmidt, were apparently not happy with these claims.

We are not going to enter into a public debate with Fred Anderson or his lawyer, they said in a statement yesterday.

The SEC investigated the matter thoroughly and its complaint speaks for itself, in terms of what it says, what it does not say, who it charges, and who it does not charge, the board said. We have complete confidence in the conclusions of Apple’s independent investigation, and in Steve’s integrity and his ability to lead Apple.

While Anderson walked without admitting or denying guilt, the SEC continues to pursue former Apple general counsel Nancy Heinen on fraud charges, claiming she was directly responsible for falsifying documents. She denies these charges.

The SEC has said it will not sue Apple over the accounting problems, it has not said its investigation of individuals is over. Apple is considered by many a personality-led business, and anything that could hurt Jobs could hurt the company more it would with other CEOs of other IT firms.

In addition to the SEC, Apple’s options practices are being looked at by the US Attorney in San Francisco. Some say that Jobs is unlikely to face charges. Others are not so sure.

Yesterday’s board statement was signed by all Apple’s directors except Jobs, who is also chairman.