Ok did you do the auto tuning? It should move back and forth and progressively get rouher then it will move onto the next stage etc.
There is a document giving rough settings to use as a base for the auto tuning.
Did it run away fast or was it relatively slow? If fairly slow then click on the DAC Offset button on the  X axis PID Tuning page and it will create an offset voltage to keep the axis still when not commanded.
You will not be able to use the MPG unless the axis is homed, so either disable your home switches then press RefAll  or actually do a Home move (press RefAll) but best to get the tuning reasonable first.
Regarding keyboard jogging, you may or may not be able to do that, depends how you have the MPG set up, do you have a MPG module? Do you have a rotary switch to select axis and  x1 x10 x 100? If so do you have an enable button for them or not?

Hood

I tried the auto tuning, but it just moved very slowly in one direction. But this started happening before I started the auto tuning.

This is the MPG I'm using for the moment:
http://www.ebay.co.uk/itm/CNC-3-Axis-4-axis-USB-HandWheel-MPG-pendant-for-Mach-3-engraving-Router-system-/251372031164?pt=UK_Computing_Other_Computing_Networking&hash=item3a86f0ccbc

How can I move it in the opposite direction, apart from putting voltage manually to the motors?

Ok first thing I would do is remove the pendant as it may be causing conflicts.
Next make sure you have the latest plugin for the CSMIO, not sure what you have but it may be an early one if from the CD, not sure what they supply now.
If you go into the PID tuning page in the plugin see if you can jog with the keys in it.
Hood

The plug in is 2.0.52 dated august 2013, I guess this it the latest version??
I've unplugged the MPG
No I can't jog from the PID tuning page, this is the same on X&Y axis.

Is the limit active? Can you get rid of the flashin RESET? Have you tried pressing the DAC Offset button and if so is it giving you a value?
Hood

Oh and the latest plugin was just last month if I recall, 052 is the latest.
Hood

Something I noticed in your xml, you have Z Home switch and E-Stop set to the same port and pin.
Hood

The limit switches aren't active as yet, I need to rewire how they are currently wired, although the home switches are.
your right about the Z home, error on my part.

I've managed to move the machine back manually, but each time I enable power to the motors, the bed moves in same direction again. although faster this time (Really quick!!)

I can reset the flashing button

if I press the DAC offset button, the value of 0 still remains the same. after winding the machine back I'm now getting the error, epid fault, press reset on mach screen

Ok try inverting the encoder and see if that helps.
Hood