Sorry but How can we help if you are having private conversations that we are not privy to.? and only giving us half the information.!
Either keep it all on the Forum or not at all because your always going to get conflicting info if we don't have all the facts.

If you want my advice then throw the bloody hacked up BOB in the bin, spend £5 on a new one and start again. Or better still invest in a Ethernet controller and dump the parallel port altogether.!

Doddy is correct that if you trip a limit in Mach3 then it should say "Limit exceeded" not "Emergency Stop" we know E-stop and Emergency stop are the same thing, but If it say's E-stop then you must be using the same Pin as the E-stop for the limits. Otherwise it would say "limit exceeded", when the pins are shared E-stop will always take precedence over limits in the messages. However in diagnostics you will see all the LED's light together if they are using the same pin.