I have the same problem too at times. My most frequent problem is that it will still lock/unlock but the horn option turns off or on whenever it feels like it. I've replaced my battery and made sure everything is plugged in good. I'm thinking it might have to do something with the remote?

Btw...are you using the stock stereo or aftermarket? I have a kenwood set up with a special plug that has both the new and stock radio plugged in at the same time so I can keep my keyless and dome light.