I use light flow and I've noticed this happening too.
Sent from my Galaxy Nexus using Tapatalk
It doesn't occur with Lightflow, tested it just now and it's not blinking while on a phone call. You may have gotten a notification and swiped it away earlier without actually going to the message/email/phone call and it will continue to blink until you actually go check out the specific notification. Don't know if this is a bug with Lightflow or if it's intended as a way to remind you that you disregarded a notification earlier.