I'd venture that you have most likely run across the 
filename limitations of the common CD filesystem 
ISO9660 with Joliet extensions: 128 characters in a 
name at max.  I've seen numerous cases were websites 
will have more than that in their name or path.

I've run into the same problem with some burns of my 
digital camera photos which I organize into a folder 
structure several layers deep, some folders have long 
descriptions.  Only fix is to shorten the 
filenames...or zip up the files (WinZip/WinRAR/etc.) 
and burn the Zipped version instead.  You can then use 
a program called ArjFolder (free, okay) or ZipMagic 
(retail, quite nice) to view them without unzipping 
them.