It is usually due to two factors. The first is the asymetrical shape of the heeled hull. Most hulls are only symmetrical when sailed relatively flat. The second is that as the boat heels over more, the center of effort, is no longer above the center of lateral resistance, but outboard of it, since the mast is no longer vertical. This adds a significant lever arm for torquing the boat around the center of lateral resistance and adds to the problem.
Any rudder that is turned more than about 10-15˚ from the direction the boat is headed, is going to stall and act more as a brake than as a rudder. Many boats generate far too much weather helm than is possible to compensate for using the rudder. This is why many boats will actually sail faster and flatter in heavy winds when reefed, since they won't be heeling as much with reefed sails.