Steve Jobs is supposed to be out from under the threat of criminal charges because of the backdating that went on at Apple even though he picked favorable dates, according to what his hometown paper, the San Jose Mercury News reported Sunday. The news tickled Apple’s stock Monday.

However, the Merc may be have been a bit premature in suggesting Jobs was home free.

The SEC, which said it won’t pursue any further action against Apple, brought civil charges Tuesday against Apple’s former lawyer Nancy Heinen and the company’s ex-CFO Fred Anderson.

Anderson immediately cut a deal that – for a price – will keep him out of the dock but in wiggling out from under he implicated Jobs.

After settling, Anderson issued a statement through his lawyer that should be of interest to the US attorneys still investigating Apple.

He said he told Jobs there would be charges to pay if a batch of so-called Executive Team Grants made in 2001 were backdated and that the award would need the board’s prior approval. Jobs reportedly told Anderson that the board had given its approval and would verify the grants.

The statement says, “Mr. Anderson understood that the board of directors, which consisted of sophisticated corporate executives of national stature, including the former chief financial officer of IBM, verified the January 17 date by signing in early February 2001 a Unanimous Written Consent [UWC] with an effective date of January 17. It now appears the board may not have given the necessary prior approval to the grants, contrary to what Mr. Anderson understood from Mr. Jobs and from the board’s signing of the UWC with an effective date of January 17...”

So much for Apple’s cover story that Jobs didn’t know anything about the accounting implications of backdating. And there’s Pixar.

Anyway, Wednesday after the market closed but before Apple posted its numbers the Apple board and its brand names Bill Campbell, Millard Drexler, Al Gore, Arthur Levinson, Eric Schmidt and Jerry York came out in force on Steve’s side issuing the following statement:

“We are not going to enter into a public debate with Fred Anderson or his lawyer. Steve Jobs cooperated fully with Apple’s independent investigation and with the government’s investigation of stock option grants at Apple. 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. We have complete confidence in the conclusions of Apple’s independent investigation, and in Steve’s integrity and his ability to lead Apple.”

Heinen is charged over a grant of 7.5 million shares made to Jobs in 2001 and the 2001 Executive Team grants Anderson is talking about that was made to top Apple executives including herself.

The SEC says Heinen had minutes of a board meeting that never took place created out of thin air respecting the Jobs grant.

The authorities nailed Anderson, who left Apple’s board months ago when the backdating issue came up, for not catching Heinen’s alleged shenanigans but he’s agreed to pay the option gains he personally made on the stock – around $3.5 million – and a $150,000 fine to avoid a court appearance. There will be no admission of any wrongdoing.

Heinen’s lawyer called her plight a “misunderstanding of the activities of Apple.”

Apple said in December it would take an $84 million charge to correct its accounting. The two Heinen-Anderson grants meant the underreporting nearly $40 million in expenses.

If Jobs had just taken the options when initially offered, his shares would be worth about $4 billion today, the Merc remarked. With all the finagling that went on, what he got to thank him for saving the company is worth about $494 million.

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