I am pretty much brand new to this, I recently bought a Procut plasma table, and use mach3 to run a "Geckodrive 540" controller.  I recently restored the program and lost all the configurations that were loaded for me, and need help straightening out a little.
  My first question is
  1.  Two days ago my machine was in basic working order, and since my restore all my motors are running either the wrong direction, or on the wrong axis, i havent moved the physical connections, so my problem is in either the "ports and pins motor outputs" or the "Hotkeys"... generally when running my table around I would use my keyboard arrows to move my x and y and (page up and down) to run the z.... now thats all *********ed!...  Can anyone give me some basic pointers on reconfiguring or getting any basic presets back?

If you lost your configuration (xml) file and do not have a back up you will just have to set every thing back up.  When you bought the machine, did it come with a profile already set up?  If it did, have you contacted the seller you got it form to see if they could provide you with the file you need?  They probably have a back up of it.  Setting the profile up isn't bad at all but requires you know the machine pretty intimately.  Do you have any docs on it such as wiring diagrams, specs, etc.?  Does this link help? http://www.machsupport.com/docs/Mach3Mill_Install_Config.pdf  I know how overwhelming it can seem if your new to this but we'll get you going.

Brett

I'm guessing its set up somehow in a saved file, I just don't really know anything about the computer.
  On the gecko website they have a link to a .xml but I don't really know how to run that program. Or what it does.
 There are a few different mach 3 icons on my desktop, one for milling, and one for plasma.
And one i think is an installer. I think I'm going to try to reference the other files to see if the configurations are in there.

Like I said, mechanically it's all set up, for some reason I just think my jog controls or hotkeys are all messed up and I can't get them to switch back to the normal set up .
 

 Where would I find the saved files if they were on the computer. And if Infact I find them how do I use them to set me back up?

I have sent you a personal message.  Up at the top of this page by your name under user info you will the see messages shortcut.

Brett