A thought did pop in my head during the night.. I never checked if files would load even though then filenames were wrong..
I have a feeling that things might be right, but, the FAT tables shouldn't be byte swapped. That's OK in theory , it would explain a few things.. But how the heck would hardware work out where FAT tables are stored on the drive ?!
Edit:
So what I read so far is FAT is fixed at the start of the partition . I guess this theory also explains why HD10 is moaning about issues writing to the boot sector as that shouldn't be swapped either.
Assuming PCs can't use more than 1 partition on a CF card (maybe someone knows ?) Then it may be possible to turn off byte swapping during the first few sectors on then drive, or basically root and FAT sectors.
I think as the filenames on ST & PC both end up the same, I that it proves they are already both in the same format already, and not swapping them is the correct way. But the actual data needs to be swapped... and of course the command registers etc remain not-swapped also.