I can't see all the files on the new CD-R, help?

There's a couple of possibilities: either they aren't there, or they're there but you can't see them. Looking at the disc from different machines (e.g. Mac and PC) should give you some idea.
Out-of-date versions of MSCDEX have been known to "forget" certain files when browsing a disc. If you're using DOS or are using the "real mode" drivers from within Win95, make sure you're using the most recent version of MSCDEX.
Old versions of certain CD creation programs would occasionally omit things when asked to burn a large number of files. These problems haven't been reported for some time, however.
If you were burning a multi-session CD, read the next section.