do you use the ide-fix hardware device or just the software?
Just software.
What size HDD are you copying to and from? I use IDE-fix to connect a CD drive to my Amiga, does it also have another use?
I've copied from two sources. First is Seagate 74 GB disk. I couldn't format this one (It was discussed there
http://www.amiga.org/forums/archive/index.php/t-57927.html ), as I learnt it was because Seagate HDDs mishandle IDE ports. Finally I copyed content of my old 4GB HDD with dd, but I couldn't use any other free space.
Second source was a 1GB HDD. So I made enough partitions on my new HDD (20 GB IBM Deskjet) and copied files from first and second source HDDs. All those partitions are PFS/3.
As I told before when I start from that 74GB Seagate with 20GB IBM as slave everything is OK: I can make partitions, format them, copy files etc. When I start with sole IBM HDD connected I can use only first 4GB, though boot partition on this HDD has all files copyed from that Seagate one.