Well looking over the diagram technically it shouldn't run in either case.... So obviously his wirings a bit different (aftermarket it sounds like).

http://www.hemmings.com/images/mopar-5-wire-diagram.gif

In any case there's no reason to try to run the stupid MSD balast there's nothing wrong with the factory 4 prong ballast. Go get one, plug it in and tell us if there's any difference...

Edit: wait that's a 5 wire ECU...well in any case ditch the stupid MSD ballast and run the 4 prong... then go check your ignition switch wiring.