I found an error in the default configuration for a Printrbot Simple Metal. The starting script consists of:
G28
G29
G28 results in the head going home to the back left corner, then moving diagonally to a somewhat more central location and settling there. The subsequent G29 operates in a displaced coordinate system such that the y-coordinate tries to move off the front edge of the printer and hits against the end stop.
Looking in the Repetier configuration that was provided with the printer, I find a starting script of
G28 X0 Y0
G29
When copied into the Simplify3D starting script, this works correctly.