Okay. Here is what I have figured out about Cura. It uses some of your machine settings and parameters in the Basic and Advanced tabs to place some code at the beginning of the gcode file along with the starting code you have manually entered. For example, if you check the box for heated bed, it inserts code to start the bed heater. If you also have that in your start code, then these commands will be duplicated.
I decided to enter all of my machine settings manually using the Start/End Gcode tab, which means that I had to make some changes to prevent Cura from also inserting these lines and duplicating code. On the basic tab I set printing temperature to 0. In Machine settings I set E-steps per 1 mm filament to 0 and I unchecked the box for Heated Bed.
No guarantees that this will fix all Cura issues, but you can tweak the start code all you want without worrying that Cura will insert contradictory code.
Here is my start code taken from Cura:
[code];Sliced at: {day} {date} {time}
;Basic settings: Layer height: {layer_height} Walls: {wall_thickness} Fill: {fill_density}
;Print time: {print_time}
;Filament used: {filament_amount}m {filament_weight}g
;Filament cost: {filament_cost}
M92 E600.000000 ;set steps per mm
M190 S65 ;Uncomment to add your own bed temperature line
G21 ;metric values
G90 ;absolute positioning
M107 ;start with the fan off
G28 X0 Y0 ;move X/Y to min endstops
G28 Z0 ;move Z to min endstops
;G1 Z15.0 F{travel_speed} ;move the platform down 15mm
M109 S225 ;Set extruder temp
G1 E10 F400 ; prime the nozzle
G90 ; use absolute coordinates
G92 E0
M82 ; use absolute distances for extrusion
G1 F3900.000 E-3.00000
G92 E0
G1 F9000
;Put printing message on LCD screen
M117 Printing…[/code]
Here is the first few lines from a gcode file sliced with Cura using the above starting code:
[code];Generated with Cura_SteamEngine 13.12
;Sliced at: Sat 08-03-2014 22:27:03
;Basic settings: Layer height: 0.2 Walls: 1 Fill: 20
;Print time: #P_TIME#
;Filament used: #F_AMNT#m #F_WGHT#g
;Filament cost: #F_COST#
M92 E600.000000 ;set steps per mm
M190 S65 ;Uncomment to add your own bed temperature line
G21 ;metric values
G90 ;absolute positioning
M107 ;start with the fan off
G28 X0 Y0 ;move X/Y to min endstops
G28 Z0 ;move Z to min endstops
;G1 Z15.0 F9000 ;move the platform down 15mm
M109 S225 ;Set extruder temp
G1 E10 F400 ; prime the nozzle
G90 ; use absolute coordinates
G92 E0
M82 ; use absolute distances for extrusion
G1 F3900.000 E-3.00000
G92 E0
G1 F9000
;Put printing message on LCD screen
M117 Printing…[/code]