Perhaps people see "coder" as a larger term encompassing programmers (where "program" would be an application), scripters (things like javascript, php, python) and maybe hackers? I'm not sure.
I think they're both just general terms that are roughly analogous. I think coder and [moreso] scripter both seem just ever so slightly negative, though that may be a subconscious association with terms like 'code monkey' and 'script kiddy.'