I don’t know the AS/400 specifically, so take my answer with a pinch of salt (and if I’m wrong, fellow answerers, feel free to delete this). That said…
Many filesystems carve disk into blocks. This makes it easier to create the TOC for the files, but it can also mean that portions of the drive go unused. For instance, let’s say a drive used 8-byte blocks, but you had a 6-byte file. That file would have a physical size of 6 bytes, but a logical size of 1 block, or 8 bytes. Essentially, to get the logical size you have to round up from the physical size to the next largest block.
I’m even less sure of this, but I can imagine this problem may be exacerbated if the file is fragmented, as each one of those fragments has that rounding problem. Imagine an extreme case, where our 6 byte file is fragmented into 6 files — now the physical size is 6 bytes, but the file takes up 6 blocks (one fragment per block), and each block is 8 bytes — 6×8 = 48 bytes logical size.
Again, not sure about all this, but it might at least give you a starting point. HTH.