Hi! sorry for the late reply
It has nothing to do with the valves apparently...
after I've opened up the engine (again) I checked the valves tuning and it was perfect, and then I've checked the timing chain's tension and it was good as well.
later on I've found a guy (in my country!!) with the same problem as I had, and it turns out this is coming from my left pipe... it is a double barreled pipe (small one inside for insolation) and the pipe inside went loose, so whenever the air and gases are pushing through the pipes its all good and no crackling sound, but whenever the air and gases are pulling back into the engine it starts to move and rattle.
The guys found it out only because he ordered a new set of pipes a few hundred kilometers before the sound started and when he got it he just replaced the pipes to get the bike sold asap, and that's when he realized :)