I remember reading in Amiga Format that Windows support for the ISA card was a little weak, but I'm not entirely sure. That may have only been for reading Amiga floppies, though. And those problems may have been corrected by now.
I've got a MK3/PCI in my AmigaOne, but I haven't tested any of its floppy compatibilities yet.
The MK3 driver CD is pretty vague, but there are definitely drivers for the card for 2K and 9x. The only operating documentation on the CD is in German, so I can't tell what formats are usable. Maybe Jens Schoenfeld could help clear things up...
EDIT: From the Individual Computers website:
Even the 800KByte disks from older Macintosh computers can be used in standard 1,44MB drives, although the original drives have rotated their disks at variable speeds. You can get a complete overview over the supported formats in the technical data. Even if the format you desire is not yet supported, it only requires a driver update to get new features out of the controller.
I think this is going to be a manual upgrade....
