Jim,
From what I read it's not the output voltage of the regulator but the voltage that the regulator is receiving thus the extension between the battery and the regulator would have some voltage drop (according to Ed). I gather that once the received voltage from the battery is the same, they will be used equally but BUT, I do agree with you. How would the receiver know that the power is unequal if the regulator is sending the same regulated voltage....hmmmm.

Either way, I check both packs every flight. I'm very careful about doing that. I'm going to go and hook up my handy dandy Ed Alt programmer again now and double-check the numbers. I did originally set both to 6.0V