[BlueSideUp]

On the aircraft I fly there is a way to disable the aural warnings and every airplane I've flown has some prescribed method to do so. However you'd have to have a serious case of rectal cranial inversion to take off or operate an aircraft with the system disabled unless the emergency procedures specifically told you to do so (like when you're in the air and getting incorrect warnings).

Our aircraft has two flap settings for takeoff, 8 and 20. Our SOP calls for a flaps 20 takeoff normally and a flaps 8 takeoff when required by the performance data. The flaps 8 setting can look pretty close to retracted since it's only an average of 8 degrees of extension across the wing. It's possible that the flaps were set at 8 and the crew realized that they should be set to 20 for your particular takeoff conditions. Other airlines operating the same aircraft use flaps 8 for all takeoffs except when 20 is required, the opposite of our airline. If you were riding on an ASA Delta Connection CRJ going back to Atlanta then that would be the case, they normally use a flaps 8 setting for takeoff.

Also at the top of one of the screens you will see a T/O CONFIG OK in green as long as all of the conditions are met for takeoff. Perhaps one of the crewmembers saw that the message was missing before entering the runway and lowered the flaps. While it isn't good to miss such a big item in the checklist it sounds like they caught it well before they would get all of the aural warnings.

Most airlines retract the flaps completely after exiting the runway and leave them up while in the ramp area to prevent damage. The CRJ had a requirement to inspect the flaps for twisting before every takeoff so many operators left them at the takeoff setting when on the ground. Most airlines have added a twist detection system so the flaps can be brought up all the way, some of the cheaper operators have decided to not install the system. Just a little TMI for you...