No, it's the Android software (Samsung's flavored) in your phone doing it.
Manufacturers often make changes to Android, even the most basic things.
On HTC's the LED blinks for a limited time like that too. On Samsung's, only when the screen is on.
( if my memory serves )
As for your comparison with missed calls and sms messages -- those apps are built into the phone's software and may be treated in a special way.
One more thought: I believe Samsung phones have some sort of "energy saving" mode (somewhere in the phone's settings app), maybe that's what it is.