Microsoft investors may be disappointed that Ford Motor chief Alan Mulally won't be riding to their rescue. More worrying is how the long search for Microsoft's next boss has exposed what seem to be divisions at the top about who should be running things.

Mr. Mulally's announcement that he plans to stay at the car maker sent Microsoft's stock down nearly 2% on Wednesday. The market reacted similarly on Dec. 13, when it became clear Qualcomm President Steve Mollenkopf, another rumored contender, wouldn't be going to Microsoft.

Mr. Mulally's move is especially noteworthy. Many on Wall Street and in technology media had essentially anointed him as the favored candidate. The drumbeat of preapproval suggests some on Microsoft's board held this view. But co-founder and Chairman Bill Gates hinted strongly at the company's annual meeting in November that he was seeking a leader with a strong technical background, seeming to nix the possibility of someone such as Mr. Mulally.

It is unlikely that any new chief would be selected without Mr. Gates's blessing. And whoever it is will report to a board that includes Mr. Gates and Steve Ballmer, two ex-CEOs with strong personalities and visions of their own.