I had the same problem, but I was using el cheapo Ikea CR2032 batteries w/ the bumpy backside. I bought some better quality Energizers (w/ smooth backsides) and they worked! I also had to clean the contacts inside the remote w/ a cotton swab and rubbing alcohol. They appear to be super sensitive to oils from your skin.
My remote issues went away and both remotes now work great (one had quit working altogether and the other was giving "key ID incorrect" codes in the car).