First thing you need to do is replace the original LED on your mpu board. The original is old and faded and sometimes it's really hard to see things with them. Put a brand-new red or yellow or green, doesn't matter the color, just something new. This will help a lot.
Every board I work on gets a new MPU LED. This is a five cent part and takes 10 seconds to install. It needs to happen for you to have a clear understanding and a clear view of what the board is doing. For example in the video Andrew posted above, a new LED would've gone a really long way and showing you what happens. If he had a new LED we would see the initial flicker in the video. Personally I pick an LED color that makes sense for me. It also is a unique color so that when I work on the board years later I can say, hey that was my work that's that color LED I always install.
Next you need to understand how the LED works. When you power the board on the LED is on. The software running is what turns the LED off. This takes about 50 ms for the software to get up and running. So the initial flicker is definitely a flicker and not a flash.
With that in mind you can count the flashes which are more like genuine flashes. if you have a new LED on the board it's a lot easier to see all the stuff, and see what's going on.