However, since Anchorage Airport was closed due to weather conditions, Captain Moen had to land at nearby Elmendorf Air Force Base, as planned ahead of time.

Captain Moen had not re-lowered the flaps after raising them to prevent icing, during which time First Officer Markestein remarked "Okay, let's not forget them."

Immediately after the plane left the ground, the cockpit stick shaker began to vibrate, a safety feature to alert pilots of imminent aerodynamic stall.

Any time a 707's flaps aren't extended (lowered) for takeoff, upon the crew applying thrust, the takeoff warning system should sound an audible warning signal (horn), but this didn't happen on flight 799, because Pan American had failed to implement Boeing's January 31, 1967 Service Bulletin 2384 recommending the warning system's throttle actuation point be reduced from 42 degrees of thrust-lever advancement to 25 degrees in order to work correctly in cold-weather conditions (where very cold air provides greater lift, as was the case with flight 799, hence less need for thrust): Pan Am's operations engineering group had decided (incorrectly) that Boeing's service bulletin was inapplicable to Pan Am aircraft, for reasons they never documented.

The NTSB recommended that checklists be revised so that items critical for safe flight be accomplished prior to takeoff, and that Boeing Service Bulletin No.

Unfortunately, it took 18 years for NTSB's recommendation in the 1969 crash report that "Air carrier cockpit checklists to be reviewed in an effort to ensure that each list provides a means of reminding the crew, immediately prior to takeoff, that all items critical for safe flight have been accomplished" to be implemented.

After the August 16, 1987 loss of Northwest Airlines Flight 255 for similar reasons,[5] NTSB recommended that Federal Aviation Administration (FAA) convene a human-performance research group to determine "...if there is any type or method of presenting a checklist [that] produces better performance on part of user personnel," and for the FAA to recommend checklist typography criteria for commercial operators.