It's metal fatigue.
If you repeatedly bend and unbend a strip of metal it gradually loses bending strength (i.e. it starts to 'go floppy'). Repeatedly winding the clock's spring, and allowing it to unwind, has made it 'floppier' than it used to be. So it's now easier to wind the clock than it used to be.
Since less energy is required to wind it up, the spring stores less energy. The regulator mechanism ensures that the energy is still used at the same rate as before but, since there's less energy to start with, it runs out faster.
Chris