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Steve Jobs’ e-book ‘smoking gun’: Did the DOJ pull a fast one?

PX-0055 and PX-0195. Click to enlarge.

FORTUNE — Plaintiff’s Exhibit 55, which U.S. attorney Dan McCuaig introduced with a flourish at the end of the day Tuesday, was almost too good to be true.

It was a Jan. 14, 2010 e-mail from Steve Jobs himself, and not only did it seem to support the central theory of the government’s antitrust case against Apple (AAPL), but it suggested for the first time that Jobs — not his pointman Eddy Cue — was the “ringmaster” of the alleged conspiracy to raise the price of e-books. See Did Steve Jobs give the DOJ a smoking gun?

Apple’s lead attorney, Orin Snyder, had tried to defuse the evidence on Tuesday, but the judge cut him off and his question was stricken from the record.

On Wednesday, however, Snyder slipped into evidence another government exhibit — Plaintiff’s Exhibit 195 — that on close examination looks like a small incendiary device that he plans to set off on Thursday, when Eddy Cue takes the stand.

It’s another Steve Jobs e-mail time stamped 18:21:39 — bizarrely, 90 seconds before PX-0055 — that looks like a later version the other one (same subject matter, same recipient, appended to the same Eddy Cue e-mail) with one important difference:

Where PX-0055 had language about moving “Amazon to the agent model” that supported the government’s case, in PX-0195 that language has been replaced by a version of the so-called “most favored nation” clause that tends to support the defense.

Could it be, as Snyder suggested when he introduced PX-0195 into evidence, that there were multiple drafts of this e-mail in Steve Jobs’ computer? And that U.S. attorney McCuaig chose to show the judge — and the reporters covering the case — one that Jobs had discarded?

Having written a story about the “smoking gun” e-mail, I feel like the government pulled a fast one. I can only imagine how U.S. District Judge Denise Cote — who will decide the non-jury case — is going to react.

We may find out Thursday when Snyder gets a chance to ask Cue what he knows about it. On the other hand, Cue was in the middle of the action in those six weeks in late 2009 and early 2010 when the government says the illegal plot was hatched, and there may be too much ground to cover to spend a lot of time on a single piece of e-mail.

UPDATE: Snyder never got to these e-mail, and in fact didn’t come close to finishing his cross examination. Cue will be back on the stand Monday at 9:30 a.m.

The case is U.S.A. v. Apple.

For background, see: