More specifically, the red lights start blinking when you hit a set threshold, like 10.8v. The thing is, as you fly you use variable amounts of power (heavy throttle v. descending, etc). So under heavy load your voltage may sag below your threshold level, and it will start blinking red, but when you let off the sticks, the voltage bounces back over the threshold and it goes back to green. When you're on the cusp, this is why you see red/green alternating. It's not specifically programmed to alternate, it's just responding in real time to your battery voltage.
In the end, it's as cuddley says. Once you start seeing intermittent red blinks, you are getting close to your level 1 alarm, and should plan on being on the ground shortly.