If the system only recognises fat 32 partitions which need to be set active, and if it only works with a 32 KB cluster size (or less?), that's how it is.
I have a car that runs on fuel, and believe it or not, if I try water which is so much cheaper, it doesn't work.
The hardware issues with harddisks is usually not the harddisk itself but the ide/sata2usb converter. Some work fine, others have minor issues, and some don't work at all.
The good thing about this is that most of those converters aren't very expensive.
If you have a good relation with your computershop, they might even allow you to trade a non functional one and try another one.
pre assembled usb drives are usually worse. The western digital passport for instance covers a range of usb harddisks. The latest are usb 3.0 compatible but don't work well with the wii.
The usb interface is integrated in the hardisk electronics, so you can't try another. Also, they sometimes have special features like hidden partitions with encryption software, which can't be removed easily. If you connect such a drive to a pc with the xp OS, it will ask for a specific driver which is already suspected.
Upon every ios reload, neek completely reloads. This means that the harddisk is initialised again as well. If this doesn't work fluid 100%, neek won't run stable.
Improving compatibility of harddisks is a difficult task, since the only method you have is trial and error. To do that, you need the bad functionning harddisk.to test.
We started the development of neek2o with neek rev. 168. We didn't change anything to the usb code and the way the harddisk is initialised.
I really see no logical explanation why rev. 168 would give a better compatibility than neek2o.
I do admit that some revisions of neek2o had bugs in the diconfig.bin building code, that could cause freezes during first boot.
I also see no logic in the fact that fat32 partitions only are reliable for partitions < 32GB. That's a marketing thing from Microsoft, which simply switches to ntfs for larger partitions.
NTFS has advantages like allowing a file size bigger than 4Gig, but a lot of it's extra features are unused. FAT32 is well documented and widely used, so by now you would expect most
bugs in it are found. I use my harddisc with fat32 daily for neek2o testing, and never had problems of it becoming corrupt.
If people say, hell yeah, rev.168 works, and later versions don't, I will look into it and see what change causes this behavour, but if I have to examine every rumour that floats around, I won't live long enough to create a stable user friendly neek2o.