I've been having issues using ISO CD images. I mounted AmigaOS 3.2 ISO and was able to install AmigaOS 3.2 successfully but after a reboot it was unable to read all of the contents of the CD. The icon was missing and so were several files and folders. If I copy a fresh version of the ISO it works perfectly. I suspected that the installation of the OS from the ISO image somehow corrupted the ISO. To confirm my theory I reinstalled the OS just to see if it would corrupt the ISO file again. And it did. I did an MD5 checksum of the ISO image before and after the install and they were indeed different.
Another issue, not sure if related, on another hard disk with AmigaOS 3.9 I wanted to see if it could play the video files on the AmigaOS 3.9 CD. They play for about a second before stopping with an I/O error.