Last week end I put a voltage regulator on my cummins in stead of the pcm working the alternator because of jumping voltage and a no charge state some times so i hooked it up and left the black thing on the alternator and when it would try to charge it would interfere with the voltage regulator and the check engine light with a no charge state and the light would go on and off on when it was trying to charge and off when it wasn't trying to charge re turning to a charging state so i took the black thing off and now it will charge all the time but the check engine light still goes on and off so how do i fix it should i put the box back on and switch the posts around so maybe when it tries to charge by itself it will maybe not interfere pls let me know this is buggin me and i dont want to ruin my pcm totally or mess up the wiring or something thankyou

Ps With the box on check engine code 12 with out it code 15