Do the front-panel buttons work, too? Are you running 2.0beta7?

If the front-panel buttons don't work, and you are running 2.0beta7, there's nothing wrong with the remote. It's a bug in 2.0beta7. Either live with it until Beta9 is released, or go back down to 1.03 which is stable and does not have this bug.

Wait. You said you rebooted the machine several times, so that's not it. The bug would have been cleared by a reboot.

Hmm. Are you absolutely certain the battery is not dead? How do you know the battery is not dead?