Still not sure what you are meaning by manual?
What version of Mach are you running?
Are these tests with the port cable connected or are you still doing it unconnected?
Can you attach your latest xml as I am unable to replicate your problems here so maybe something has changed.
Hood

I hope you had a wonderful Christmas. To make sure I get the latest XML file Please give me instructions on how to obtain these.. Also I do have the port unconnected. The Version is 2.0

When I first bought this machine it was only half wired for CNC. You had control of x,y,and z with CNC but the spindle's both mill and Lathe, speed and direction were controlled by the VFD. That cycle was termed Manual. There is a method to program the VFD so it changes the P codes to run CNC which of course is the best way to run it. Dan Mauch helped me wire the machine to run full CNC and if you remember, His instructions caused us grief because he had  the red and green wire switched and we couldn't get speed control ect. JT sent me a wire diagram that pointed out the mistake.
Since I was grabbing at straws I tried things in the manual mode not thinking it was only spindle controls and such that it controlled

Ver 2?
Hood

Maybe this is what you want. Demo version, R3.043.066

Ah ok thats more like it, still cant replicate your issues here but if you attach your latest xml I will try again.
Hood

To make sure I get the latest XML file Please give me instructions on how to obtain these..

I have windows XP on that computer

Open Mach and on the main page look lower right and you will see the profile name. Look in the main Mach3 folder for a file of that name with a xml ectension.
Hood

try this

Well again, although a different xml from previous, I do not have a problem with it. Just to confirm I am understanding correctly, when you command a move from MDI (machine plugged in) such as G1Z1 the axis DRO only goes to 0.001 but the motion of the actual motor continues?

Also you mention E-Stop is the only way to stop it, you do not have an E-Stop set up in Mach (you have it to Port 0 ) so how is your E-Stop connected on your machine or are you meaning something else when you say E-Stop?
Hood