I made this .Xmodmap.
! free up right-Alt for remapping
remove mod1 = Alt_R

! Right-Alt remapped to Super
clear mod4
keycode 115 = F13
keycode 108 = Super_R
add mod4 = Super_R
I saved it in home, log out and logged back and got a Super key assigned at Alt_R.
This is the output I got with xev for the keyboard
 state 0x0, keycode 108 (keysym 0xffec, Super_R), same_screen YES
When I restart the system though, the Alt_R works as Alt not as a Super key.
xev will still say that this is Super key, though (the output is the same as the one above)
 state 0x0, keycode 108 (keysym 0xffec, Super_R), same_screen YES
Running manually
xmodmap .Xmodmap
will produce
xmodmap:  .Xmodmap:2:  bad keysym in remove modifier list 'Alt_R', no corresponding keycodes
xmodmap:  1 error encountered, aborting.
so the key is defined as Super, but is working as Alt. Loging out and in back will make Alt_R to work properly, without any further tweaking.
Disabling automating login will make the PC show the logins screen after boot, and after loging in the Alt_R will work properly, too.
This makes me thing there is a step that is needed for the .Xmodmap to work at 100%, which is triggers only when the login screen is shown.
Any ideas how to fix this - I dont need a login screen at start, so I will like to have my key working without the need to enter password every time I boot.