As dstock mentioned, my system stops charging the aux. battery after about 20 - 40 minutes and I can not override the controller to manually connect both batteries.
There is an interesting thead I found here:
http://www.jkowners.com/forum/showthread.php?t=82078
Which supplies some information about how the Jeep's system works.
The upshot of that thread is that there was a grounding issue, which, due to the way the system operates, caused a severe over-voltage.
From what I gather here, the problem with NL seems to happen more with Jeeps.
So what I'm thinking about what you just described, is that the NL is disconnecting because the Jeep's charging system in raising the voltage up over 14.7v and keeping it there.
Why that would be happening - if indeed it is - after driving for a while...
Well, it's probably that that's simply how long it's taking for the charging system to bring the aux battery up to a surface charge that high. In other words, the (relatively) low aux battery is drawing down the bus voltage, the charging system is keeping the alternator turned on to try and achieve whatever it's trying to achieve, and it takes, as you described, 20-40 minutes for the aux battery to get there.
Okay, that's all well and good and is normal behavior. The odd behavior would be that the charging system is not backing off and is keeping the bus voltage very high, and this is why the NL won't reconnect.
So then the questions would be, A) IS it holding a high voltage, and B) Why?
I'd first want to see real no-BS voltage measurements while driving. (I've done that before by taking a length of cut up extension cord and running it from the battery into the vehicle and then hooking up a multi-meter and setting it on the dash and watching it all day while I drove.)
If it really is holding a voltage over 14.7v, then the effect would that the main battery is (possibly) being overcharged, and the aux is (certainly) being undercharged.
Then the next question would be why is it doing that, and according to the thread linked above, that could likely be a grounding issue which is confusing the computer.