beinghuman,
hopefully this clears some things up...
You are correct in saying that the stalling angle is decreased by lowering flaps and cl max is increased aswell by the lowering of flaps. The fact that flaps being lowered decreases the stalling angle however seems contradictory.
A highly cambered wing will stall at a higher stalling angle than an aerofoil with little camber. The reason for this however is due to the smooth and gradual change of shape of a cambered wing, something like on a STOL aircraft.
When lowering flaps however, whilst the camber is increased, the change of shape occurs abruptly at the rear of the wing due to the flap slab. That is to say, the mean camber line is increased only at the rear of the wing.
The change of pressure gradient with flap extended is abrupt rather than smooth and laminar for a clean wing. For this reason, flow seperation occurs at a lower angle of attack than with a clean wing.
The camber has increased, but it has increased in an inefficient way, at a cost to the stalling angle when flaps are extended.
Hope this clears things up.