I thought to use TSmuxer to do that, but don't know if cutting files without knowing which kind of frame is the first and last of each piece, the result will be compression-artifact free... probably yes, but as I still I need to know is WHAT is making it wrong, and because I tomorrow I will work, sleep, and few things more, I'll be not enough concentrated to work onto other projects, so let's work this ol'PC of mine! (^^,)

I have a lossless "digital intermediate", and it's perfect, so I suspect the problem was arisen when I tried to open a file encoded with lagarith, the same codec used in the "DI"...

So, to whom it may concern, if you need to make a perfect x264 encoding, this is what I have learned so far:

use a lossless "digital intermediate" whenever possible, it will spare you a lot of encoding time (up to 30/40% in my case) - sometime, it's the only way to avoid problems
if you make a two pass encoding (strongly suggested), leave the .stats and .stats.mbtree files alone, until you are 110% sure the final encode is right; it will spare time if you will be forced to re-encode, as you could do only the second pass
never open a video file that uses the same codec of the "digital intermediate" - if possible, try to avoid to open ANY audio/video file
if you encode using an avisynth script, do not use any software that will use an avisynth script - like virtualdub, but also VLC, MPC etc.
if you need your final file is BD compliant, be sure to use all the right settings

"That's all, folks!" Hope this will help someone!