Well, in the end I had to return my phone to the shop today, as it's still under warranty.
I'm curious if there are going to do something with it, fix it, replace, or just return back, as I'm not really sure if they will find any errors, but I hope they will.
Just in case, I flashed the original WM RUU from HTC, and yesterday, while playing with it for a while, it rebooted a couple of times, and was quite hot as well.
Last week-end I've been to Lisbon, were we had 32 degrees at some points, so my phone was freezing every 5 minutes, when I put it in front of the blowing AC fan from the car it could work like that for hours without any issues, but I suppose it should work like that always and in all conditions. This made me understand that the overheating due to a faulty board could be the root cause of all problems. I suppose that even the bad blocks appeared after the overheating issue appeared
I will write here an update when I'll get my phone back from the service.