Reprap prusa i3 Y and Z axis swapped when printing GCODE files
Sounds like your slicing program is not set up right.. Or more likely your printer isn't.

I would use Pronterface 

I use simplify 3d, but the best free software is Slic3r. 

Try those then report back. Honestly I think you might not have it wired correctly. With pronterface tell it to move X. Then try moving it and manually holding the endstop. Then if it does not stop try going tho incorrect way with that endstop still pressed. If you find that your reversed you will need to correct this with your firmware. If I knew this was a ramps board you could reverse the wires, but lets do it in firmware as I am not buying you a new board. 

After that you should work. Software wise we just made sure your interface and your slic3r work and talk the same language. Those two I know will not be doing anything funny. After that report back if it is still not working.