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Janus Capital Management just can't catch a break.

After a long battle, Janus was thought to have

finally wrested control from parent

Stilwell Financial

(SV)

in September, with the restructuring to be finalized in December.

Now, though, a Boston hedge fund that is Stilwell's biggest shareholder has raised its stake in the company and hired an investment bank to evaluate whether Stilwell's plan to cede control to Janus is in the best interest of shareholders.

Highfields Capital Management, which now owns a 7% stake in Stilwell, hired Blackstone Group to go over the details of the arrangement. The move was disclosed on Monday in a filing with the

Securities and Exchange Commission

. Highfields said last week it increased its stake to 7%, up from 5.9%.

"Highfields has a history of doing this; it's part of how they see themselves as investors," says Morningstar stock analyst Rachel Barnard. "They see themselves as helping the company run its business. But these moves tends to be on the unfriendly side."

Recently, Highfields has challenged management decisions at

Adelphia Communications

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and

Reader's Digest

(RDA)

.

Barnard expects Highfields' focus to be on Stilwell's ownership of

DST Systems

(DST)

as well as the sweet deal Janus gets as a result of the reorganization.

In an effort to reduce its huge debt, Stilwell said in October that it would consider selling its 33% interest in DST Systems, a provider of investment management services. It's likely that Highfields would want Stilwell to more aggressively seek to unload DST, both to pay off some debt and focus on its core asset management business.

The company, though, will take a huge tax hit if it sells its entire stake outright, Barnard noted. That's a wrinkle that nobody seems to have a solution for yet.

In addition, Janus Capital Management "got pretty much everything they wanted with a cherry on top," Barnard says. "They got accelerated vesting of their stock, higher than average compensation levels, performance bonuses, and one of their own running the new company who doesn't seem inclined to upset the apple cart." (Mark Whiston, president of retail and institutional services at Janus, is slated to become chairman and chief executive of the reorganized firm.)

Janus has brushed off any suggestion that the Highfields involvement is problematic.

"We're certainly open to receiving input from Highfields about strategy, as we would from any other shareholder," says Janus spokeswoman Shelley Peterson. "We believe the previously announced reorganization of Stilwell Financial is in the best interest of shareholders, and we remain focused and committed to completing it."

"I don't think the Stilwell/Janus reorganization is in jeopardy," Barnard says. "But I wouldn't be surprised if it gets ugly."