I had this problem too - it started a few days ago and was driving me nuts! I tried wiping the system cache, even a full a factory reset all to no avail, tried everything I could think of and of course searched the Internet forums and tried many suggested fixes, but none of them worked for me....
It ended up being Lookout Mobile Security (antivirus app). I've had it on my devices for a long time, but it was recently updated and that's when the blinking blue light came on whenever the screen was off and wouldn't stop. It also 'overriding' normal notifications for new mail etc - ALWAYS blinking blue LED, no matter what - even when charging. (Normally steady red then steady green when 100% charged). Nope ONLY blinking blue.
I noticed also that there was always a Samsung default new message 'whistle' sound everytime I rebooted or turned the phone on, but no new messages to be found anywhere from any apps...
Then it finally dawned on me tonight... The only notification message that was there after reboot was the usual 'Everything is ok' notification from the Lookout app...
So I went into Lookout's Settings and the only 'Notifications' option it has is found at the bottom of the list. It's just a check box for 'Show sticky status icon' [Always show the Lookout icon in the top bar so you know it's running in the background].
I simply unchecked that box and lo-and-behold... no more blinking blue notification LED, nor do I hear the mysterious new message whistle after reboot or turning the phone on.
Not saying this will work for everyone, but if you have Lookout Mobile Security installed and your blinking blue light problem started recently, there's a good chance it'll be the culprit. It had me all but totally stumped.
