I'm running into the same issue. Basically when I run the job, the platform heats first, then the extruder. Once the extruder has reached temperature, the print starts and right away the extruder stops heating and drops in temperature.
I've attached a temperature curve which shows a normal run at number 1 and a bad one at 2.
Setting the temperature manually works just fine and if I interpret the graph properly it looks that the extruder heater is just being shut off.
I'm not sure why some prints work and others don't.
Here is the G-code on the failed print:
(M190, M104 and M109 seem to be set properly)
; generated by Slic3r 0.9.9-dev on 2013-05-24 at 21:13:18
; layer_height = 0.1
; perimeters = 2
; top_solid_layers = 3
; bottom_solid_layers = 2
; fill_density = 0.20
; perimeter_speed = 30
; infill_speed = 40
; travel_speed = 150
; nozzle_diameter = 0.35
; filament_diameter = 3
; extrusion_multiplier = 1
; perimeters extrusion width = 0.59mm
; infill extrusion width = 0.98mm
; solid infill extrusion width = 0.59mm
; top infill extrusion width = 0.59mm
; first layer extrusion width = 0.42mm
G21 ; set units to millimeters
M190 S60 ; wait for bed temperature to be reached
M104 S187 ; set temperature
G28 ; home all axes
M109 S187 ; wait for temperature to be reached
G90 ; use absolute coordinates
M82 ; use absolute distances for extrusion
G1 F1260.000 E-1.20000
G1 Z0.300 F9000.000
G1 X15.310 Y11.230
G1 F1260.000 E1.20000
G1 X15.540 Y10.930 F900.000 E1.20650
Any help would be appreciated.