The two commands
M107 and M104 Snnn
are always placed before the custom g-code.
Why?
Is there any way to disable this or do I have to manually edit the .gcode file to remove them?

M107 is Fan Off
M104 S### is Set Extruder Temp to ### degrees

I wouldn't worry about them unless you are trying to do the reverse (turn the fan on or maintain the current temp setting)

Quote
marnargulus
I wouldn't worry about them unless you are trying to do the reverse (turn the fan on or maintain the current temp setting)

That is what I am doing i.e. altering the temp in the g-code but I just realised I can put in M104 S0 to negate the effect anyway.

M104 S0 ; negate default
G28 ; home all axes
M190 S45 ; set bed temp & wait
M140 S55 ; set final bed temp
M104 S190 ; set extruder temp
M116 ; wait for both temps to be reached

Just set the Temperature and First layer temperature settings to zero and Slic3r will not output any M104.