Ok, now I got it. It's the CD with the printer drivers on it. Sorry, my mistake (I slept too little last night).
You say that certain files can be seen only by one OS at a time
That seems possible to me only if that CD is multisessioned written, a session under Widnows and one under Linux. Even so, Linux should have no problems in reading it as Linux can see NTFS but Windows cant see ext2,3, etc.
Or you maybe you mean that some files can't be used
under the other OS. That would make more sense.
However, if you're in the first situation, I can't help you, sorry, I'm a sort of n00b myself.
Good luck anyway!