Car runs after main switch by battery is off

Perhaps...but not 100% sure!!

MSD run-on? :scratch: Although it's stated not requred, are you using a Bal resistor with you 6al. On page 9 of MSD instructions it states that "very little voltage" is required to keep the unit powered to supply power to your coil. (even with the key off) I would think your alt passing current through your voltage reg is just enough to keep your 6al going. It also states if you have a Chrysler with run-on (then use the dual resisitor)