When an M104 command is sent from the SD card it doesn't turn on or off the led graphic beside the extruder in the machine control panel. Note that this doesn't affect the real leds on the viki LCD panel. I noticed this because I manually turn on the heated bed and extruder before a print to get them up to temp and when the print was finished, the extruder was turned off but the led graphic beside the extruder was still in the 'on' state. If the M104 command is sent from the communication window command line or if it is sent via USB then the led graphic works as it should.
I created 2 small files to test this:
M104 S190 T0
M104 S0 T0
Try running the files from USB and you will see that it works properly but if you put them on the SD card and run them from there you will see the problem.