You probably need to go one or two steps further on the motor to ensure the flag
is in the opto interrupter properly. this is the standard way that any motor
finds its home position (like in a floppy drive seek mechanism). If this is not
acceptable to you, then arrange the opto to be slightly further out.

Another thing that is often done is once the opto senses the flag, then the
motor is stepped to a given phase. This allows things to move slightly with
temperature around the opto flag and its mountings, and only requires
temperature compensation on a minimal number of close tolerance components.