Well, install PFS2 and see.
You didn't mention how big partitions you used for the 4.3 and also whether 4.3 was what the computer sees or what's written on top of the drive.
The original Amiga scsi.device will wrap at 4096 megabytes, and if you use FFS, your maximum partition size should be 2GB.
The PFS2 direct scsi version cures both these problems, but if you want to play it safe, you might want to have a smaller boot partition (say 300MB?) and then store everything else on the bigger partition(s).
Oh, and always quick format your hard drive partitions..
