I am trying to set up my home switches and thing doesn't seem to go well. I have 5 proximity sensors wired for x and y axis. X- Home, X+, X Prime, Y- Home, and Y+ to the Gecko 540.

X-Home and X+ are wired together to Input 3 pin 12.
Y-Home and Y+ are wired together to Input 1 pin 10.
X Prime is wired to Input 2 pin 11.

On the diagnostics screen, M1++ Limit, M1—Limit, and M1Home light up whenever either of the Y sensors (plus or minus) is tripped. M2++ Limit, M2—Limit, and M2Home light up whenever either of the X sensors (plus or minus) is tripped. M4Home lights up whenever the X prime sensor is tripped. However, when I press ref home, my Y-axis moves first and continue to move even when the sensor on the Y-axis is tripped. It will only stop when I trip the X-axis sensor. Then, the X-axis motor and the A-axis motor move in the opposite direction and will only stop when I trip the Y-axis sensor. What am I doing wrong here?

What are you meaning by X prime?
Hood

X Prime is the sensor on the A-axis side. I have 2 motors for the X axis, one is X and one is A.

Maybe this picture should help to clarify...

Do you have the A as a slaved axis in Mach?
Have a look on Genral Configs page for homing slaved axis options if you do.
For reversing axis directions for Homing use the Home Neg option on Homing and Limits page (from Config menu)
Hood

Yes. A is set up as a slaved axis for X. My problem is the X-axis supposes to home first then Y. However, the Y homes first but only stop when the sensors on the X-axis is triggered.

Mach3 screen also shows Y axis is homing first. Isn't X-axis supposed to home first? As far as I know then sensors will be triggered on order starting with X and then Y.

Can you attach your xml and I will look.
Hood

This may be a wild question but how do I get the XML file?

When you have Mach open you will see lower right the name of the profile you are using. Look in the main Mach3 folder for a file of that name with a xml file extension. Copy it to your desktop and rename it to helijet.xml and then use the additional options button on the reply page to browse to your desktop and attach to the forum.
Reason you need to rename is the forum only accepts a file name as an attachment once, so if you are using a standard profile that name will already have been uploaded to the forum.
Hood

Here is the xml file