The lights have stopped scrolling up and down but are not lighting up when I run the software.

From Fretlight Knowledgebase

First of all, make sure that the Fretlight cable is FULLY plugged in on both ends to the computer and the guitar.

If you have the Fretlight footswitch plugged in, try clicking either button. Sometimes the footswitch may be setup up to "Turn lights on/off".

Go into the preferences of whatever software program you are using make sure that all strings are turned off. Many of the software programs have the option to turn off certain strings, to help memorization of linear scales. Ensure all strings are turned on and try again.