novice82, It sounds like one of the axis is going to a home position. The fact that it doesn't stop at the mechanical limit switch sounds like the X, Y, and Z axis plugs are mixed up where you connected them to the machine control cabinet. The Y axis is the longer travel up and down the table along the guides under the edge of the table. The X axis is up on the gantry above the table and moves across the table. On my machine the Y axis moves 35 inches and the X axis moves 25 inches. If The X axis is pluged into the Y axis motor it wil not see the Y axis overtravel limit switches because it is looking for switches on the X axis which is not moving. You may have the Z axis pluged into the Y axis plug and the machine thinks it is raising the spindle and looking for spindle travel limit switches.
I would not load a program until the jog functions are all working the correct axis and directions of travel. You must also go to settings/ manufactory and type the password "ncstudio" to get to the perameters menu. If power on is moving the axis motors unplug them at the control box so they don't move and look down the list of perameters for something which would automatically home the machine. Then plug up one axis and make sure it moves with the correct direction input (X+ moves to the right and Y+ moves away from the frequency controller and start button end) When all three axis are on the right button if one or more moves the wrong direction you can reverse it by checking the box in the perameters list for that item. My machine was correctly and clearly labeled in english and it all jogged the right directions. You must also set the number of steps per millimeter of travel. The NCstudio runs on metric input G-code. I save my files as "Mach3MM.nc and except for a warning "G64 ignored" it runs great.
For your problem I would only plug in the Z axis and make sure Z+ raises the spindle and Z- lowers the spindle. Then add the X axis which moves across the table, and finally the Y which moves the long travel down the table.
If you have everything wired correctly and nothing looke odd in the perameters menu you might contace saleCNC.com for software. I have delt with them and recommend them. Also on this forum I got mine working from advice I got from
"butterknife". To troubleshoot your glitch it would be helpful to know just what you have "clicked" on after double clicking the NCstudio icon to launch the program.
wizzardworks