The original IDE driver of the Amiga cannot see more than the first 4GB of the HDD. To circumvent this limit you need two patches: an updated driver (scsi.device) and a new file system. You only have a new file system, so it does not work yet.
The best choice of an updated IDE driver for use with PFS3 is IDEfix97, but it costs money.
http://www.vesalia.de/e_idemax97.htm
There is a free patch for scsi.device here:
http://os.amigaworld.de/index.php?lang=en&page=37
But it only works with PFS3ds because PFS3 does not use the 64bit commands offered by this patch.
Note these:
- the boot partition has to be inside the first 4GB of the HDD (as you already experienced: you 128MB partition is fine)
- you must not format partitions beyond the 4GB barrier of the HDD. You can use quick format for all partitions anyway.
- there are many many programs which do low-level access to the HDD and don't support large HDDs. Using them may lead to total data loss. This includes the format program as mentioned before.