A bit of a mystery -
If you were to login to a guest session can you change the launcher to autohide? (thru the right click on Desktop , ect.
Assuming you are using unity, not unity-2d, you could check with
should return 3 like
env | grep -i "^desktop_session" && env | grep -i "xdg_current_desktop" && env | grep -i "compiz"
So if in a ubuntu session (unity) can you write to this file?,
if so look for this line & change red to 1 (blue will be different, doesn't matter
Then save & log out/in
<entry name="launcher_hide_mode" mtime="1364055559
" type="int" value="0
if you open ccsm from a terminal what profile does it show being used, should say -
Profile : unity
Worst case you could also try resetting unity -