Okay, I figured out the problem, and it's not quite what I expected! Here goes.
Nero 6 has a new "feature" which they neglected to tell us about... if you have files with the same name, even if they are not in the same directory, or have different file sizes, then when the files are burned (all files are burned) the index will be modified so that one of the duplicate files will not be viewable [:I] This causes the verify feature of Nero to fail, since all the files appear to be slightly different for some reason (possibly due to the indexing changes) and whatever duplicate files that were burned, will not show up in the verification. However, all the data is still there, so the CD-R/W still shows that it was filled to the proper capacity.
So what does this mean to a user? if you are burning albums of music, and you have two directories with two songs with the same title, say perhaps one band is doing a cover of the same song, or perhaps it is a remix. Even if the files sizes are different, if the file *names* are the same, then one will be written out of the index of the CD. *OR* if you are a game designer, and you put your own game onto a CD-R, you might have the same graphics library or similar file in several different directories... well, all but one of these files will disappear.
I will be contacting Nero about this new "feature" and requesting that they implement a warning/request so that you have the option of removing the file, or letting the duplicate stay.
I'm a little sad to say the only reason I figured this out was because WinISO has the same "feature" only it *WARNS* you about it when it activates.
...Well, at least the mystery is solved!