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Paul Allen and Bill Gates in 1981. (Microsoft photo)

In telling the story of his early days with Bill Gates, a new memoir by Microsoft co-founder Paul Allen appears to be writing a rocky new chapter in their relationship.

The Wall Street Journal reports this morning that a raw portrayal of Gates in Allen’s forthcoming book, “Idea Man,” has “created a rift” between the two men. The first excerpt was published online last night by Vanity Fair magazine, with previously untold details about the formation of Microsoft and Allen’s time at the company. That includes a story about him catching Gates and now-Microsoft CEO Steve Ballmer talking behind his back about diluting his equity in the company because they weren’t happy with his contributions.

But more than that, the book seeks to correct the impression that Allen was a mere bit player in the formation and development of the company. In the excerpt, Allen writes at one point, “Our great string of successes had married my vision to his unmatched aptitude for business.”

Gates acknowledges Allen’s role but questions his retelling, taking the high road in a written statement to the newspaper: “While my recollection of many of these events may differ from Paul’s, I value his friendship and the important contributions he made to the world of technology and at Microsoft.”

The Journal reports that Allen’s book may also be rewriting history in some cases. From the paper …

Mr. Allen’s unflattering account of Mr. Gates in the book is already making waves within the tight circle of early Microsoft alumni, with several people who know both men privately expressing confusion about Mr. Allen’s motivations for criticizing his old business partner and questioning the accuracy of Mr. Allen’s interpretation of certain events. Mr. Allen, for instance, puts himself in meetings that people familiar with the meetings say he never attended. In one case, Mr. Allen visits Palo Alto, Calif. to help woo a computer scientist who would later become one of the Microsoft’s most important programmers. People familiar with the meeting said it was Mr. Gates who made the visit. (Allen spokesman David) Postman said that he isn’t aware of any errors in the book.

The hard-nosed financial dealings — such as the scene with Gates and Ballmer — probably won’t surprise anyone who has worked at big companies, or read a Gates biography.

But the surprise is Allen’s willingness to tell the unvarnished stories of those early days, at risk of alienating his longtime friend — particularly in an era when much of the world sees that friend as a benevolent philanthropist as opposed to a cutthroat monopolist.

In that way, the book dovetails with the lawsuit filed last year by Allen against Facebook, Google, Apple and other web giants. That suit brought to light the early work by Allen’s Interval Research lab on some of the foundational technologies of the Internet — but it ticked off pretty much everyone in the tech industry in the process.

So what’s going on here? From covering him over the years as a reporter, my understanding is that Allen was deeply affected by the “accidental zillionare” label first given to him in a 1994 Wired piece. The magazine story called Allen’s wealth a “lucky trick of time and place, and particularly of his involvement with Bill Gates.”

Allen seems to be on a campaign, of sorts, to correct that impression. The only question is whether his legacy will survive it.

Todd Bishop of GeekWire can be found on Twitter and Facebook, when he’s not thumbing through old copies of “Hard Drive” and “Gates.”

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