@Castellen:
I just remembered that I had a somewhat similar issue once:
I was about to install CGX v4 on my A2000. At that time it had no CD-ROM, but it had a network card, so I put the CGX v4 CD in my linux box (the cd-drive on the linux box is shared with samba) and mounted it on the A2000 with smbfs. The installation went fine and after a reboot CGX v4 was up and running.
Anyhow, when I tried to install the 4.3 rc5 upgrade, it failed when patching some files for an to me unknown reason - I even tried executing the patch lines manually in a shell without success. For some reason, the patch-utility just didnt want to work normally when accessing the CGX v4 CD as a smbfs networked volume.
It ended up in the A2000 being equipped with a CD-ROM to be able to successfully install the 4.3 rc5 upgrade

.
It got me thinking - can it for some wierd reason have anything to do with the CD-ROM driver/device/filesystem?
Just for the record, when installing the upgrade on the A2000 I used a SCSI CD-ROM with the stock WB3.1 L:CDFileSystem and on the A4000 I have used an IDE/ATAPI CD-ROM and the
Atapi PNP package.
/Patrik