When you tell the floppy drie on a PC to say, read a track. The drive then reads the raw data off the disk. Then the floppy drive controller is a microcontroller that then decodes the raw data sending back to you the decoded data you want. On the Amiga, when you do this, you get sent back the raw undecoded data from the disk, you then must decode it in software. This does give the cpu a little more burden (that isn't very amiga like but that's the way it is) but it does make the amiga more flexible (I think some games even had their own custom encoding format).
So Amiga disks are encoded differently from PC ones so the PC floppy drive controller can't understand what it's getting from the disk.
srg