When u start the car, does the "KEY" light on the dash flash green? If it does, its warning u, ur remote battery needs replacing. Happened to me few weeks ago. Replaced batteries, problem solved...no more KEY light flashing in green.
I too have a 2nd keyless remote and i haven't used it in more than 6 mths and the battery is dead on that one so its not unusual, ur 2nd one is flat too.