Did you ever solve this?
I've had similar problems before. Infact a CD I burnt using AmiDVD on OS4 had one dir that did not show on Workbench but did exist! :-?
But It think the problem is the read only protections bits. You see, although it is logical for a CDROM disc to be read only, when a dir is copied to the HD it will also be read only and thus non-writable! :-o
That said, I don't know how to stop a disc from being unreadable,but kmnow it can happen. For example, I wanted to check out the X1000 boot CD in my Mac. It mounted it but the disc was completely empty! :-o