Okay enough scripts, we can learn that junk as we go so lets start scripting with GMT. First, if it works for Bob and not for you, your defaults are probably different. They are kept in a file called ~/.gmtdefaults. There are tons of them and you can find out what they are and what the mean reading the man page for gmtdefaults.
Unrelated to defaults is directory organization. You will be glad if you set up directories and subdirectories to keep your maps, data, and scripts organized. I have something like this in ~/GMT
csh/ data/ ps/ scratch/ sh/
There is a directory for csh scripts, for sh scripts, for data files, for postscript files, and for scratch files. Do this. Trust me.