When you install Starlink you have to determine the directory of the program (set env starlink_dir /path/to/software/star, in the ~/.tcshrc file). Then, any application runs under this directory.
But, there is a limit in the number of characters used (only 40). This can cause some programs not to run at all or run very quickly (and not producing any output of course!).
So keep an eye on the length of your working directory !
[2011/05/05 NOTE: this should not be valid after Hawaiki version !]