I was using Mach 3 and a gecko 540 controller with an old PC that had a parallel port. I bought a UC100 so I could use a new laptop instead, running windows 7 64Bit. Got it all up and running except for homing of the X and A axis, which are my gantry. I can jog all 4 axis just fine, but when I home, only the Y and Z move. Then when I try to jog again, only the A axis will move. Next I went back to the old PC and parallel port and everything works just fine. I copied over the Mach files and all of the settings are the same between the two computers. Really need some help!

So that tells me that not everything is the same.   What versions of mach 3 are you running?

Do this.
On new computer copy the UC100 DLL file from the C:/mach3/plugins folder to a memory stick.
Rename the C:/mach3 folder on new computer to say C:/mach3 old

On the old computer copy the entire  mach 3 folder (yes all 200+ meg of it) to a memory stick.
Copy this to the C drive of the new computer.
So on the new computer you have a C:/ mach3 and C:/ mach 3 old directories.
Copy the UC100 DLL back into the C:/mach3 plug ins directory.

Go and download .062 version of mach3, not the 66.  ftp://machsupport.com/Mach3/
download and install with default values.  it will overwrite the core files of mach but not any settings.  This also gives you a stable version of mach that works with USB motion controllers.

now you should be set with exactly the same setup as on the old computer.  As its the old computers files. 
When you open mach for the first time, you may have to reset device selected and restart mach so you can choose the UC100

I thought slaved axes had to be configured in the motion controller plug-in?

well seeing how mach3 is a motion controller.......
Config>slave axis

I thought slaved axes had to be configured in the motion controller plug-in?

Every controller is configured differently. Read the manual.

well seeing how mach3 is a motion controller.......
Config>slave axis

Technically Mach3 is a trajectory planner, built around a parallel port motion controller 
Take away the parallel port, and it's just a trajectory planner sending motion commands to a motion controller plugin.

As Gerry says, check the manual for the motion controller, as they're all different. For example I know Smoothsteppers require slaved axis to be configured within their plugin, and KFlop needs slaved axis to be configured within an initialisation script.