Can't get Counter limit to work on HBL1660

My motor is turned by an external mechanical force for a number of turns. Then I need the controller to electrically move the motor back to the starting position. I am using open loop and progressive regen script when "motoring". In Roborun, I set the hall counter limit at 1000 and "Safety Stop" action on Max. Then I give the motor some throttle. It turns from some negative position (counter at -1000, for example) into positive, passes 1000, but doesn't stop in spite of the 1000 counter limit. Am I doing something wrong?