Hi pilotho,
why does this alert not occur with flaps down?
If you have a look at this Boeing document:
http://www.theairlinepilots.com/foru...kref/stall.pdf, on page 36 it quotes the minimum V2 margin over the stall and on pages 46 onwards gives examples of various aircraft types and their margins. You will note that the margin is only around 13% for some aircraft!
The buffet margin when clean and in the cruise is normally 30%. Therefore to avoid unnecessary distractions on take off and departure, the software is written so as not to advise you of reduced margin when you have flaps out.
The buffet warning margin may be changed to suit the operator. We used to "fudge" our cruise C of G (if conditions were smooth) to reduce the buffet margin to 25% and at high weights, permit an earlier climb . We were then limited to a smaller bank angle.