ok, hope this helps you.... I had exactly the same problem but mine was after a magnet had split in half for some inexplicable reason. I had to replace the magnet with a small neodymium fridge magnet and a 3D printed bracket.
I got into the firmware via putty/serial and set the threshold value to '20' for all filters rather than doing the automatic calibration. This tells the motor to slow down and position the filter accurately I believe.
Use the command "R5" in the terminal. Problem solved. Now it stops as soon as that value is reached on the hall sensors.
See the bottom of the instruction PDF for other very useful commands.