Crash investigators hoped the recovery of the black boxes would help them quickly make sense of the crash. Instead, the calm voices on the cockpit recorder–which contained just the pilots’ final 30 minutes of conversation–only deepened the mystery. Now, officials are working to create a minute-by-minute account of the pilots’ actions before the crash, hoping they will reveal clues that their words did not.

Salvage crews recovering parts of the plane from the ocean floor found a potentially critical clue last week. The aircraft’s jackscrew, a mechanism that moves the horizontal stabilizer up and down, was severely damaged. Some of the threads on the screw were badly stripped. Investigators believe a faulty jackscrew could have caused the stabilizer to jam–though they also say the damage to the part could have happened as a result of the crash. After the discovery, the Federal Aviation Administration ordered immediate inspections of all 1,900 MD-80s and similar models currently in use worldwide. The results were surprising, and scary. Mechanics found varying degrees of wear in four Alaska Airlines jets, and similar problems turned up in 11 planes operated by other airlines.

Investigators are also trying to figure out why the pilots turned off the autopilot about 15 minutes after taking off from Mexico, and kept it off for most of the next two hours. Flying the plane manually at high altitudes can make the ride bumpier for passengers. National Transportation Safety Board officials believe that the pilots may have encountered a problem with the horizontal stabilizer very early in the flight–well before they reported it to air controllers–and flew manually while they tried to fix the malfunction. When the cockpit voice tape begins, it’s clear that the pilots had already begun discussing stabilizer troubles.

The airline has turned over at least one tape of those conversations to the NTSB. But sources close to the probe say investigators aren’t sure they have all the information about in-flight radio contacts between the pilots and the company about a possible problem. The airline says it is turning over all relevant information to the NTSB.

As the investigation continues, the NTSB is also likely to take a look at whether the FAA may have been lax in correcting problems at the airline. For more than a year, federal law-enforcement agencies have been investigating supervisors at Alaska Airlines’ maintenance facility in Oakland, Calif., for falsifying maintenance records. (An Alaska Airlines spokesman says they are cooperating with investigators.) At one point, according to internal government documents, an FAA inspector recommended the airline be fined $8.7 million for record-keeping violations. But agency brass knocked the fine down to $44,000, claiming passenger safety was never at risk. Now some investigators want to know if the FAA, long accused of being too soft on the airline industry, may have let Alaska Airlines off too easily. The FAA says it recently assigned new supervisors to oversee the airline. A welcome change, but one that may have come at a very high price.