Ok, I disconnected the endswitches and it still happened.
What I actually never noticed before is that I could see the motor 'slipping' or stopping when I just moved the printhead around (not by hand, but from replicator using the manual control). I started experimenting adjusting the stepper motor driver potmeter, which indeed changed the behaviour, but also resulted in a burned driver, haha, I guess I was becoming a little impatient...
Then I thought, ok, will it be the driver or not? Inserting the driver from the X motor, actually resulted in the same slipping way of moving.
So here I am, 1 driver down and still a slipping y axis.. Anybody?