Issues with primary key fob

The key we usually use was acting weird (only locking sometimes, etc) so we starting using the other thinking it was just a low/dying battery. Key fob #2 has no issues. I replaced the battery in Key fob #1 and its actually seems worse, doesn't seem to respond but will start/run the car. Is it possible that its been "forgotten" by the Car's ECU?

How old was the battery you replaced it with? Brand new from the store or one you had sitting around in the package?

Brand new from store, and the red LED lights up on the remote when the buttons are pushed.