What do you exactly mean by “running bin/thisroot.sh”?
What do you get when you execute:
[bash] export | grep DISPLAY
{csh] setenv | grep DISPLAY
When you execute “root” (without the “-l” option), can you see the graphical “splash image” displayed for the first 5 seconds?
What do you get when you execute:
root-config --etcdir
root-config --prefix
root-config --exec-prefix
root-config --bindir
root-config --libdir