Ok, I found the problem to this. I use ImgBurn to create ISO images, and in my settings I selected the wrong type of CD, so it was truncating the filenames.
For those who are interested on the Options tab select "ISO9660 + Joliet" under file system. Then under the advanced tab, go to restrictions, select Joliet and select "Level X -110 Characters". This stopped ImgBurn from truncating file names, and everything is working.