2000 Honda Odyssey dead battery, transmission acting up

When the van is running about 30 or 40 it runs and shifts great. Below 30 and the transmission acts weird on shifting. Battery was dead next morning, charged battery, shifting was great. Until the battery was dead again. Took it to mechanic, he said that the codes (check engine light was on) said that the transmission was shot and something about the word ellyptical needed to be replaced. (I am assuming it that has something to to with the alternator). When the battery is charged, everything works great, yet the mechanic (got a little tuffy with me) states that the transmission is NO good.