Yes, you are quite right. When I cd to the directory where nupdf is located and call it with
# ./nupdf /path/to/my/doc.pdf
It works perfectly.
What I was trying to do before was to put the nupdf program and data folder in a directory in my PATH, then cd to my document directory, and call it from there with
# nupdf doc.pdf
What a great program! Thanks for helping me to get it working.