The Caddx system at one of my family members/customers house was doing this a while back after they had a low battery. (Of course, they said the power was out for 5 hours) Then it continued to flash for a low battery for a 35 hours later. When i got there, all I did was enter my code and it reset and everything was back to normal. Try arming and disarming or entering and exiting program mode if you haven't done so yet.
Most brand spankin' new batteries I've hooked in have never been low either. Maybe a defective battery? Or a polarity issue as George described.