Here is an explanation I've been given, I'm not qualified to vouch for its correctness, though it makes sense to me:
Lowering flap significantly changes the spanwise pressure distribution on the wing. Since flaps tend to be on the inboard portion of aircraft wings, lowering flap causes the pressure distribution to become more centralised, which decreases stability in roll. Clearly, roll stability is more crucial in strong crosswind situations since there is more chance of gust upsetting the aircraft in the roll axis, so a lower flap setting means more stability.
The higher Vref/increased aileron effectiveness metioned before also makes sense in this respect.