I updated to version 4.4. from 4.1 aswell and i have the same problem.
Sometimes when a game starts (every emulator) i must wait 10-20 seconds before the controller responds
(for example "press START to start Tetris or Super Mario Land").
But the green text, that appears when i start a game, on the botton left appears and says "Controller Xbox 360 worked".
Sometimes the controller doesn't work in a game.
On 4.1 everything was fine.
Thats probably the same problem that FuerDrauka has.
I dont belive that we are the only ones with this problem, that must be an update issue and i dont know how to solve this.
I reinstall the xbox driver but nothing helps.
Maybe someone has a solution sometimes.
Now i'll create a new partition and reinstall 4.1