OK I actually got it...
Since I only wanted to use two bulbs, I set only two leds in the "LED Configuration". And this determines how many Hue devices Hyperion is going to look for.
I changed the LED Configuration in order to have the same number as my Hue devices, and it found all of them.
Be careful though, if you set more leds than the number of Hue devices connected to your bridge, the service will fail to start.
Hope it'll help some of you!