i used to do EMG PU installs on many guitars and i remember making a mistake with the volume pots once, where it would sort of go thru the volume after the switch if that makes sense. effectively, if both pu's were selected but one volume was down, neither would work because both volumes sort of worked as a independant master. i would check your EMG wiring diagram and see if it matches the one specifically for LP's or guitars with two sets of volume/tone controls. the difference is literally switching two wires on each of the volume pots.