I have the same problem. If I have a notification waiting, it will only blink one time when I hit the power button to turn the screen off. No more blinks after that. Turn the screen on, then back off, and it blinks once and no more.
I doubt I need to replace the phone, it just seems like a software issue.
I keep finding things about LightFlow (someone said it was free, another said it was paid) but I don't see why we should have to install an app to get it to function properly.
Also, I don't have a case, so no my LED isn't blocked.