I've written a perl script to manually add courses to the mdl_course table. I run it from the command line. The script just reads lines from a text file and inserts the data directly into the database table.
It's an X-1. It works, but there are a few glitches when I look at the courses using moodle; they're not as serious as the problem you're having, though, Christofer. My guess is that the newline character in your text file is not one that is being recognized by whatever script you're using to batch upload courses, so that whatever "reads" the text file never finds a second line.