Skype‘s co-founder Niklas Zennstrom has handed over his CEO title to become non-executive chairman of the board of directors of this eBay Inc. unit, whose impact on its parent company remains an open question.

Michael van Swaaij, eBay’s Chief Strategy Officer, is stepping in as interim CEO until a permanent replacement is hired, eBay announced Monday.

Also out is Henry Gomez, who has been with eBay since 2000 and joined Skype about two years ago. After serving as general manager of Skype North America and later Skype Chief Marketing Officer, he was named its president in December 2006. Gomez will return to the eBay fold as a senior vice president for corporate affairs.

EBay acquired Skype, a provider of Internet telephony services, in October 2005 for approximately US$2.6 billion, plus an optional amount dependent on the achievement of certain goals.

From the start, many have questioned the logic behind the acquisition, suggesting that eBay would have a difficult time recouping its investment and leveraging Skype to boost interactions eBay among buyers and sellers.

In the second quarter, ended June 30, Skype’s net revenue hit $90 million, up 103 percent compared with the same quarter in 2006. Meanwhile, registered user accounts grew 94 percent to 220 million.

However, eBay CEO and President Meg Whitman, discussing the second quarter’s financial results in a conference call in July, said that, despite its revenue and user growth, Skype hasn’t achieved the desired level of “user activity.”

In August, Skype suffered a widely publicized and embarrassing outage that lasted about two days and left millions of users fuming worldwide and many openly questioning the stability of Skype’s technical platform.

The Skype management changes aren’t due to the unit’s financial performance, said eBay spokesman Hani Durzy. Zennstrom decided to step down as CEO of his own accord in order to focus on other projects. As non-executive chairman of Skype, he will serve mostly in an advisory role, Durzy said.

Gomez, meanwhile, was asked by Whitman to return to eBay and take on his new role, which will involve high-level communications and government relations tasks, Durzy said.

Durzy acknowledged that eBay is disappointed that Skype hasn’t performed as well as expected in the short term in the areas of user activity and monetization, but the company believes Skype is still a very valuable asset.

Skype will try to boost its monetization capabilities by exploring broader e-commerce options, possibly within services like SkypeFind, in which businesses are listed and recommended, and SkypePrime, a service for selling advise and expertise.

On Monday, eBay also announced that it has paid

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