What does the LED blinking on Arduino boot mean?
In my opinion your first suspicion was right. It is the bootloader flashing the LED.

This page (scroll down to the section 'Versions of the bootloader') says: 


  [...] The NG bootloader waits about 6-8 seconds and flashes the LED three times. [...]


The bootloader is signaling, that it is waiting for a new program to arrive.