A little update...
As you may recall, the reason my electronic Cummins QSB was running rough was the Balmar Duo Charge, which I had reconnected, gave the Cummins ECU indigestion. I had gone back to the Blue Seas ACR.
Nothing wrong with the Blue Seas ACR, but I never liked the idea of sharing all the charging action to house bank with a simple start battery. Tonight I hooked up a Xantrex Echo Charger.
The Echo Charger is very similar to the Duo-Charge but dumber. It simply will provide up to 15 amps of charge to the start battery whenever there is over 13v at the house battery. I believe it does this at the same voltage that is being supplied to the house bank.
Simple to install, just three wires. Once installed it started to work and upon starting, the engine ran just fine. So for now anyway, I am going to stay with the Echo Charger and following some advice that Bruce B gave me, not make any other changes right away. Another suggestion of his, remove the offending Duo Charge. That I also did tonight.
FWIW, I really like the Duo Charge and currently have two of them, one charging the thruster bank and the other charging the genset battery.