Hi Marius, thanks for the reply.
Sorry for the confusion. I simply meant that if RapidMiner is trying to download a pdf via a direct URL, such as :www.website.com/folder1/otherfolder/filename.pdf
Downloading the pdfs manually via right-click options works fine. I can also do it via another WGet application. It is just when trying to get RapidMiner to download the documents that I get the problems mentioned.