A few days before MF Global’s collapse, CFTC chief Gary Gensler wasn't convinced the bank's finances were in order, despite assurances made to regulators stationed within the bank. We all know what happened next: More than $600 million in customer money was missing from MF Global, prompting an investigation by the CFTC. Yet the agency has already been dealt a big blow. Last week, Gensler stepped away from the investigation amid questions over his relationship to Jon Corzine, his former boss at Goldman Sachs. Now, the worry is that the commission will stumble in its rare turn on center stage without its star leading the way. Gensler’s withdrawal from the investigation came despite apparently only loose ties to Corzine. The men have seen each other just a handful of times since Gensler left Goldman Sachs in 1997. Still, Gensler’s recusal puts the CFTC at a potential disadvantage as it embarks on its most high-profile investigation since its founding in 1974. Under Gensler, the commission had begun to shed a reputation as a toothless watchdog, bringing a record number of enforcement cases while writing new rules to police Wall Street. At the same time, the agency’s budget is under attack on Capitol Hill and it faces questions over its handling of MF Global. Lawyers and MF Global clients have questioned why it is taking so long to recover money that should have never been missing at all. MF Global is the agency’s biggest enforcement test yet. Whether the scandal will burnish or tarnish the reputation of the agency, as well as that of Gensler, will depend on how quickly authorities can locate the missing money and pinpoint what went wrong. [Dealbook, 11/8/11]