jjones86 wrote:And you're using the Repetier 0.92 firmware?
With Repetier firmware, there's a few changes to make in Simplify3D.
Tools-->Firmware Communication-->Communication and then in the Flow Control setting, set to Hardware Flow Control. This lets you connect to the printer.
Turn on "Wait for Temperature to stabilize before beginning build" for the heated bed and extruder(s) in the Temperature tab of the process settings. This tells the printer to wait for it to reach temperature before proceeding any further.
Then lastly, in the Ending Script for the first line, add "G28 X0 ; " (without quotes), to get the printer to home in the X-axis when done.