Had my printer working well with repG and 7.7 sailfish firmware. As it is not easy to use one exdtruder for support and one for model in repG I decided to try makerware and it broke something.

(** This GCode was generated by ReplicatorG Sailfish - 0040r24 **)
(* using Skeinforge (50) *)
(* for a Dual headed The Replicator *)
(* on 2014/08/01 11:28:47 (+0100) *)
(**** start.gcode for The Replicator, dual head ****)
M103 (disable RPM)
M73 P0 (enable build progress)
G21 (set units to mm)
G90 (set positioning to absolute)
M109 S110 T1 (set HBP temperature)
M104 S230 T1 (set extruder temperature) (temp updated by printOMatic)
(**** begin homing ****)
G162 X Y F2500 (home XY axes maximum)
G161 Z F1100 (home Z axis minimum)
G92 Z-5 (set Z to -5)
G1 Z0.0 (move Z to "0")
G161 Z F100 (home Z axis minimum)
M132 X Y Z A B (Recall stored home offsets for XYZAB axis)
(**** end homing ****)
G1 X-110.5 Y-72 Z50 F3300.0 (move to waiting position)
is hte start of the Gcode file and it is supposed to end with the head at the front left while it warms up.

M109 S110 T1 (set HBP temperature)
M104 S230 T1 (set extruder temperature) (temp updated by printOMatic)
The above two commands are stopping it working, instead of the X axis going left it doesn't move if either of those commands are sent to the printer. They are not supposed to do anything regarding the X and Y axes.

This happened after I tried printing/slicing with makerware. I have reblown the sailfish firmware and have reset defaults, I am now stuck with no clue as to why it is now printing way off where it should be. The stored home offsets are correct.