Looking at the image in post 42, You have the inputs pullup jumper set to 0V. You need to set it to the 5V end.
Also the Enable source jumper is set to enable always (pos ON), swap it to the Enable end.(it won't change anything as you have the 3 enable override jumpers in.
Since you limit inputs are active low, you need to go into the Mach3 configuration and ensure that the inputs that are using input pins 10,11,12 and 13 have the active low checkbox ticked.