Justin if the tail motor stalled, that is if it stopped turning while under power, while it was plugged into the main esc, it may indeed have damaged the esc. Usually they fail completely but it is possible for it to fail in a way to still give partial power.

I would suggest getting ahold of another 3-in-1 or a separate esc to try. It is very unlikely that your batteries are both bad, especially if you are geting the full voltage on charge.