OK465,
The stall speed ratio applies to the configuration used for compliance with the approach climb minimum gradient requirement. The AFM or equivalent should state the approach climb flap settings used for determining the climb-limited landing weights in the normal and alternative landing configurations, respectively.
I also vaguely remember a provision (but cannot find it now) that the flap select lever should not pass through a 'gated' position when going from the landing setting to the related approach climb position.