First are you still on the laptop or desktop.?
If laptop then forget it they are just too unreliable due to heavy memory management and Mach's driver really doesn't work well with most Lappy's. To use a Laptop reliably you need an external motion controler like smooth stepper, this is how laptop runs machine I use.

If it's a desktop is it a PCI PP card or built into mother board.? If it's a modern-ish PC then chances are it's 3.3V PP if so thats it there's nothing you can do about it other than use a PCI PP card. Even then you have to be carefull because some use the USB bus to simulate a PP and again don't work with Mach. If you go to the Mach forum you will find more info regards this.

Check the bios to see what the Printerport is set to EPP/ECP etc
Are you actually hooking upto drives and motors like in a full working machine or just testing on the bench.?
Does it have an Estop wired up or the BOB have a charge pump.?
Does the bob need an external supply to activate it's opto's.? some do.!
Also what are you using for a PP cable.? are you 110% sure it's a straight thru cable standard printer cables are very often not straight thru, I've even had some that tested ok with multimeter but still had some trickery built into the plug that switched signals.!!! (Drove me F'~@ing nuts)

Have you done the Mach driver test.?
Also can you post the Mach XML file your using, it will be in the Mach folder under the same name as the profile you use to load Mach.
This will make it much easier to see if it's just a PP setting issue.? I'm curious because some where you mentioned port 0 pin 0 for estop this don't sound correct and it could be that your port address is wrong.?