If the actual flap setting is not the same as that which we have programmed in the take-off performance page of the FMGS the config warning will be triggered.
Uplinker - as others have said the T/O CONFIG just checks that there is a plausible flap setting for takeoff (CONF1, 2 or 3). It does NOT xcheck the FMGC.
These guys got caught out (and the skipper thought the same as you).
https://www.atsb.gov.au/media/519998...29%20Final.pdf