On mine the red LED3 on the RAMPS board here http://reprap.org/mediawiki/images/f/f6/RAMPS1.4schematic.png and here http://reprap.org/mediawiki/images/c/ca/Arduinomega1-4connectors.png turns on when I start to cut. That is just indicating that one of the power MOSFETs is being driven. Not sure why because those MOSFETs are normally unconnected and only used for a 3D printer configuration to power the heated bed and two plastic extruders. Probably just harmless vestigial 3D printer behavior.
Did you look at your configuration.h file? That is likely the problem.