If you put flap down then that part of the wing will not stall as soon as it otherwise would,
Foxmoth, I think you will find that's incorrect for most light aeroplane designs. Flaps tend to increase the lift coefficient for a given alpha, but reduce the max alpha available (although this isn't the case with some of the more complex Fowler designs). In other words, with flaps down the aeroplane stalls at a slighter lower angle of attack (typically 1 to 2 degrees lower). Therefore, with flaps down, the inboard sections of the wings should stall with a greater margin over the outboard sections.
My explanation would be that, with flaps down, a larger proportion of the wings' total lift is on the inboard sections and there is, therefore, a greater loss of lift in the early stages of the stall. This then exacerbates the rigging/asymmetrical issues that actually cause a wing drop.