Had mine replaced with the Fob during the 07 Recall. Asked if I could have the fob as extras but they wouldn't go for it, so they gave me the batteries. Last winter, I started geting the low battery warning and as the temperature warmed up in the spring, it went away. It must have been something with the car itself because that's what was cold, not the battery. the fob never left my inner jacket pocket. It's something I intend to address next winter (because It doesn't appear now).
In short, it may not be the batteries but it may be a problem with the sensor in the car that should be addressed.
Battery probably isn't covered under warranty and might be pro-rated if it is (if they even do that for the CR2032's).
~SB