R started in terminal shell script or ESS steps on LD_LIBRARY_PATH?

This sounds like a shell init issue... and you probably want to hunt
down where LD_LIBRARY path is *set*, rather than how it is inherited.

When you log in in run-level three, you get a login shell rather than
a normal interactive shell, and your startx inherits your login-shell's 
environment, You get a normal interactive shell(?) inside 
gnome-terminal/xterm if you start at run-level 5, and finally, you get
a non-interactive shell if you run a script, most of the time.
The environments in the three cases are all different, and
sometimes security related environment variables are not inherited
by forked sub-shells, such as LD_LIBRARY_PATH; or more likely, 
LD_LIBRARY_PATH is set up for the login shell, and other shells
simply don't get it.

HTL

 From the INVOCATION part of bash's man page - assuming that's your 
login shell, otherwise, others.
===========
When  bash is invoked as an interactive login shell, or as a non-inter-
active shell with the --login option, it first reads and executes  com-
mands  from  the file /etc/profile, if that file exists.  After reading
that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile,
in  that order, and reads and executes commands from the first one that
exists and is readable.  The --noprofile option may be  used  when  the
shell is started to inhibit this behavior.

When  a  login  shell  exits, bash reads and executes commands from the
file ~/.bash_logout, if it exists.

When an interactive shell that is not a login shell  is  started,  bash
reads  and executes commands from ~/.bashrc, if that file exists.  This
may be inhibited by using the --norc option.  The --rcfile file  option
will  force  bash  to  read  and  execute commands from file instead of
~/.bashrc.

When bash is started non-interactively, to  run  a  shell  script,  for
example, it looks for the variable BASH_ENV in the environment, expands
its value if it appears there, and uses the expanded value as the  name
of  a  file to read and execute.  Bash behaves as if the following com-
mand were executed:
    if [ -n "$BASH_ENV" ]; then . "$BASH_ENV"; fi
but the value of the PATH variable is not used to search for  the  file
name.
=========

R started in terminal shell script or ESS steps on LD_LIBRARY_PATH?

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