Most power windows don't have any limit sw, the motor stopping is everything being run to a bind and the motor stalling. The same goes for one touch express down, when the controller sees the current go high it shuts off power. ( Low rent systems use what amounts to a thermal circuit breaker in the switch. ) It is good practice to let off the button just as the window hits top or bottom.

Your car may or may not have any sort of limit sw but I really doubt it has one. The thumping is likely the motor gear slipping on the window regulator. The window regulator has a 1/3 of a gear on it and the teeth on the up portion are probably worn out or the motor has worked lose from the regulator.