I contacted Hyperion and they said that the charger should work OK with the engine running. They also gave me a series of questions to answer about while chargeing.
Before I attempted to use the (old) charger with the engine running I tried the new charger (same charger but A/C D/C version). I used the computer software to make sure the user setting were the same.
The new Hyperion EOS0720i Net 3 (A/C D/C version) charged perfectly with the car engine running and not running. So it turns out the original charger is defective.
In fact when I was trying to charge with it again with the engine running it really malfunctioned. First it over charged the lipos then when I switched to storage mode to get the lipos back to a lower cell voltage state the display flashed and it stopped working completlely!
So, it wasn't the car charging system, or the setting, it was the charger it was just giving up the ghost. As I said before I really can not be upset because I have really gotten a lot of charging/storage cycles out of it in the past 3 or 4 (maybe longer) years since I have purchased it.
I will not hesitate to buy another Hyperion charger, in fact I plan on ordering another one of the Hyperion EOS0720i Net 3 A/C D/C versions as a back up to the one I already have.
Thanks everyone for your input and help!