I'm no electrician... but if you push 500mA on two batteries to charge, isn't that like charging with roughly 250mA each? My i2 charger pushes 500mA per battery and my i4 pushes 750mA per battery when charging only on 2 bays out of 4 bays. Anyways, my i2 and i4 take a long time to charge, which makes me think charging two batteries simultaneously on 500mA would take a really long time.
About the balancing... again, I'm shooting in the dark with too much common sense
the charger can sense the combined voltage of the two batteries in parallel config, doesn't the potential problem arise when one battery hits full and other one is not there yet, let's say you have your two batteries at 4.2v (full) and 4.0v (not full), the combined voltage is 4.1volts, so the charger keeps charging both batteries and basically trying to overcharge the one battery which is already full?
About the balancing... again, I'm shooting in the dark with too much common sense