Open up Repetier-Host, load your .stl file, click the Silc3r tab and click "Configuration".

When the window opens up, click on the ""Printer Settings" tab and click "Custom G-Code" from the left side menu.

Make sure under the "End G-Code" section that G28 is listed there. G28 is your homing G-Code. That will move all your axis to the home position.

I think by default it says G28 X0, which means it will only home your X-axis. Y and Z will stay in the same place.

Try that and let me know how it goes.