Yet Van Natta resigned last November, just a few weeks before the company's December IPO. At the time, Zynga insiders said that Van Natta had always planned to leave the company after a year or two. However, to leave just weeks before an IPO looks suspicious. With all the drama surrounding the company since its IPO, it now looks even more suspicious.

This is the second high-profile COO departure from a troubled Internet company in the last year. Former Groupon ( GRPN) COO Margo Georgiadis resigned only five months after joining the online coupon company. She immediately returned to Google.

Why is it that Pincus at Zynga and Andrew Mason and Eric Lefkofsky at Groupon have had such a hard time keeping people?

There's always a bit of a cultural struggle between those at young entrepreneurial start-ups and those from more-established businesses.

Early-stage companies crave credibility, and it helps burnish their images if they can lure executives from secure jobs at established and successful companies. It sends the message to the media that the start-up is a more desirable place to be than the more established places.

Yet people coming from bigger companies are used to structure, processes and more resources. For them, coming to a start-up can be a little frightening when it seems like decisions are made willy-nilly and the founder CEO is flying by the seat of his or her pants half the time.

It can be equally frustrating for the folks at the start-up when they see an "established" executive come in and start talking down to them. These executives can also be seen as too bureaucratic and too slow in making decisions.

With Zynga, it's clear that Pincus didn't do his homework and make sure that Van Natta and Schappert would fit in at the company.

There also probably was something about the executive culture at Zynga that rubbed Van Natta and Schappert the wrong way. Mark Pincus certainly must have been instrumental in the development of that culture.

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