I can't seem to recharge more than one battery. I did a battery upgrade, so I have three available batteries, but the normal recharge only fills up one. I can get another battery to charge up by using an item, but I would think I should be able to recharge them. Am I missing something?
Technically it's not "the first" battery that recharges, it's just one. If you eat up to your max, the last bar will recharge as long as you don't use any of the second-to-max.
To complicate matters, it seems eating a multiple-battery item (which supposedly restores two energy) will actually only restore your current battery plus one more. So if you have three batteries, you're halfway through regenerating the first, and you eat a two-battery item, you'll only end up with two batteries (as opposed to the expected two and a half, with the half regenerating).
TL;DR - wait for your batteries to recharge before eating anything!