It's just a guess, of course, but it could be the choices you made when you create your CD/DVD images. While the CD9660 filesystem is an ISO standard, there are extensions needed for Windows, and extensions needed for Unix-like systems. They are different.
Windows uses "Joliet", and Unix-like systems use "Rock Ridge." Be sure to build your ISO images with Rock Ridge extensions, or they won't be usable.
See
http://en.wikipedia.org/wiki/ISO_9660 for more details.