The 06 Dip has an Intellitec IRD (Isolator Relay Delay) on the main circuit board in the front run bay. The way it works is fairly simple. Basically, what it does is close your main isolator relay in the battery compartment which combines the two banks (just as if you were holding down the battery boost button), allowing the alternator to charge both banks at the same time. This happens when the genset is off, and the IRD detects more than 13.3 volts on the 12v system for a period longer than 12 seconds (which would normally be the case when the alternator is properly charging the chassis batteries). It will open the isoloator relay if the voltage drops below 12v and then close it again (after a short delay) when it again detects an excess of 13.3 volts on the system.
For this system to work, there has to be power to the isolator relay actuator circuit. That is fed by Fuse #55 in the front run bay, so you want to check to see if that fuse is OK. (It should be labeled "AUX START".)
This system does charge both banks from the alternator, but it would not be as efficient, as the 120v charger is when plugged into shore power, or you are runnng the genset.
You will find more details on this system here on my web site
. Also, here is a link
to the IRD service manual which contains a trouble shooting guide that you might find helpful.