I've found many solutions but I do want to understand why this happens. I use English (US, International with dead keys) layout because I am a Portuguese speaker, and it's better for me not to change the layout all the time, not to mention I'm used with the US layout and key positions etc.
Yesterday I re-installed Xubunt 16.04.1 64bits and after installing the packages bumblebee and bumblebee-nvidia, I ran into this issue - again - of every reboot the layout is changed to simple English (US), where the special accents that exist in the Portuguese language. To make them, I'd press the key and then the letter, but with this layout that's changed after each reboot, by pressing the special character will simply print it immediately.
In the Settings > Keyboard > Layouts is set to the option I chose during installation, by default, but still, it insists on change.
Curiously, the previous installation of the system took around two weeks or three for it to happen, while this time, the same day.
Why does it happen? I know it's not only me.