Just trying to get a handle on your problem...
...you followed the procedure for reprogramming the keys after replacing the batteries (i.e. placing the key in the ignition and turning to position II for a few seconds so the computer can reinitialize the key chip)?
Also check the orientation of the batteries in the key housing. I have had mine stop functioning for no apparent reason until I readjusted the battery contacts, and verified that the batteries were installed properly.
I have two key units that were handed to me when we purchased our car (used), but only one of them works anyway. Replacements are $100+.