help with home and limits

[wilkies]

i have a home made plasma machine, i have the proma thc using 3 pins emergency stop on 1 pin and the last one is on the 3 home switches,also in line with with the 3 limits,i have the homing turned on in mach ,and off for the limits, now the problem is when i home one of the axis it stops before reaching the home switch i sometimes have to click twice before it reaches the switch home ,dont think mach3 knows where the axis is at. now this also does this when cutting out a part. any one know the cure.or a way to run the limits. its a 6560 with the 9 pin -5 for the limits 4 for grounds. thanks dave