Keyless Entry Red Light malfunctions

Some time ago I broke a fob and had to have it replace by the dealer. They charged me for a fob but couldn't get the car to accept the new one. They took a week and ended up replacing the car computer free of charge. Since then I haven't had any problems.

Now though a couple of times I hear the car locking and unlocking in the garage and when I look at my fob the red light is blinking continuously. When I try to unlock or lock the car with the fob buttons, they don't work. The other fob does work, but the first one doesn't. If I get into the car and try to start the engine, it doesn't start. If I open the locks with the other fob, then it will start. It's like the car is in some kind of mode encouraged by the fob.

My plan is to replace the battery and see how that goes, but from reading other posts I'm not sure how useful that will be. It's not a big deal, the only reason I carry both fobs is for emergencies. But it's odd. I occasionally hear the car's alarm go off too which I take to be the panic mode maybe triggered by the button being pushed in my pocket maybe? Annoying but it doesn't happen too often.

Any suggestions?