Ok this makes absolutely no sense to me but I repeated the problem and fix over and over and it keeps working.
So I restored my TWRP back up and then restore google accounts without the Back Up option.
All was good. I restarted because only after a restart you know if something you did made you lose the Sound Enhancements.
Played a youtube video and all was good.
So decided to fix the time cause I noticed that it was wrong.
So went to Date & Time settings and checked the Automatic date & Time and Automatic Time Zone option.
Rebooted the phone and BOOM I lost the Sound Enhancements (S.E from now on), again!
Went to Date and Time and unchecked both options, played the Youtube video again (not need to restart when "fixing it") and once again S.E works.
Why in the world is this even related?!
At first I though it was maybe location based but I can still leave the correct settings for my area as long as those options are not checked I can enjoy S.E for flac files and other apps like youtube.
Please somebody else test this because its retarded but I tested it 4 times and always got the same result!
Gayest quote ever from MST3K!
"You know Captain, every year of my life, I grow more and more convinced that the wisest and best is to fix our attention on the good and the beautiful...if you just take the time to look at it."
My Galaxy Note Games & Apps previews YOUTUBE channel