Well,
Lets go away from headphones to say cars for a moment. You get a brand new car, they recommend having the oil changed at 2000 miles. This is because the parts are all cycling together for the first time and everything is beginning to sync (and giving off small metalic shavings) and become accustomed to fitting together and moving as they should.
Back to headphones, the driver is much like a piston. The driver itself moves and the diaphragm needs to break in to allow it to do this in an efficient way. The diaphragm starts out stiff, kind of like a leather purse, then as the driver moves the diaphagm becomes more supple and flexible allowing it to move properly.
Technically, after a lot of hours like 20000 or so, maybe more, I could forsee the diaphragm becomming overly worn, or other various issues arising, so that may be an uber extended burn in for it to be worsened =).
Dave